diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 5c308f36..07909b27 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,7 +19,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.2.26 + container: obolibrary/odkfull:v1.4 # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/.gitignore b/.gitignore index 8855ab6a..0aa876fc 100644 --- a/.gitignore +++ b/.gitignore @@ -50,3 +50,4 @@ src/patterns/pattern_owl_seed.txt src/patterns/all_pattern_terms.txt target/ +src/ontology/core.owl diff --git a/annotations.owl b/annotations.owl deleted file mode 100644 index 8f184ce9..00000000 --- a/annotations.owl +++ /dev/null @@ -1,338 +0,0 @@ - - - - - - - - - - - -]> - - - - - - - - - - - - - - - - editor preferred term - - - - - - - - example of usage - - - - - - - - - has curation status - - - - - - - - definition - - - - - - - - - editor note - - - - - - - - - term editor - - - - - - - - - alternative term - - - - - - - - - definition source - - - - - - - - - imported from - - - - - - - - - expand expression to - - - - - - - - expand assertion to - - - - - - - - first order logic expression - - - - - - - - elucidation - - - - - - - - temporal interpretation - https://oborel.github.io/obo-relations/temporal-semantics/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - shorthand - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - axiom holds for all times - - -## Elucidation - -This is used when the statement/axiom is assumed to hold true 'eternally' - -## How to interpret (informal) - -First the "atemporal" FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. - -## Example - - Class: nucleus - SubClassOf: part_of some cell - - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) - -## Notes - -This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - relation has no temporal argument - - -## Elucidation - -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. - -## Example: - - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm - - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y) - - - - - - - - - - - ready for release - - - - - - - - pending final vetting - - - - - - - - requires discussion - - - - - - - - curator note - - - - - - - - diff --git a/chemical.owl b/chemical.owl deleted file mode 100644 index 935ce1ce..00000000 --- a/chemical.owl +++ /dev/null @@ -1,39 +0,0 @@ -Prefix(:=) -Prefix(dc:=) -Prefix(obo:=) -Prefix(owl:=) -Prefix(rdf:=) -Prefix(xml:=) -Prefix(xsd:=) -Prefix(cito:=) -Prefix(foaf:=) -Prefix(rdfs:=) -Prefix(swrl:=) -Prefix(swrla:=) -Prefix(swrlb:=) -Prefix(subsets:=) -Prefix(oboInOwl:=) - - -Ontology( -Annotation(dc:description "RO chemical module."@en) - -# Object Property: obo:RO_0002260 (has biological role) - -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002260 "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)") -AnnotationAssertion(rdfs:label obo:RO_0002260 "has biological role") -SubObjectPropertyOf(obo:RO_0002260 obo:RO_0000087) - -# Object Property: obo:RO_0002261 (has application role) - -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002261 "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)") -AnnotationAssertion(rdfs:label obo:RO_0002261 "has application role") -SubObjectPropertyOf(obo:RO_0002261 obo:RO_0000087) - -# Object Property: obo:RO_0002262 (has chemical role) - -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002262 "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)") -AnnotationAssertion(rdfs:label obo:RO_0002262 "has chemical role") -SubObjectPropertyOf(obo:RO_0002262 obo:RO_0000087) - -) \ No newline at end of file diff --git a/core.json b/core.json new file mode 100644 index 00000000..d6ada61e --- /dev/null +++ b/core.json @@ -0,0 +1,1025 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/core.json", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/license", + "val" : "https://creativecommons.org/publicdomain/zero/1.0/" + }, { + "pred" : "http://www.w3.org/2002/07/owl#versionInfo", + "val" : "2023-02-19" + }, { + "pred" : "http://xmlns.com/foaf/0.1/homepage", + "val" : "https://github.com/oborel/obo-relations/wiki/ROCore" + } ], + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-19/core.json" + }, + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "lbl" : "continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "lbl" : "occurrent", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "lbl" : "independent continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000006", + "lbl" : "spatial region", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "lbl" : "process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "lbl" : "disposition", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "lbl" : "realizable entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "lbl" : "quality", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "lbl" : "specifically dependent continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "lbl" : "role", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "lbl" : "generically dependent continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "lbl" : "function", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "lbl" : "material entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease is realized in this disease course" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is realized in this shattering" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is realized in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is realized by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "realized_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realizes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease course realizes this disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation realizes this investigator role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this shattering realizes this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occurs_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "site of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000141", + "lbl" : "immaterial entity", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "lbl" : "is concretized as", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "lbl" : "concretizes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this cell derives from this parent cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this nucleus derives from this parent nucleus (nuclear division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent cell derives into this cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent nucleus derives into this nucleus (nuclear division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is location of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my head is the location of my brain" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this cage is the location of this rat" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "location_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "located in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is located in my head" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this rat is located in this cage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "located_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_2D_boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "lbl" : "member of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "is member of is a mereological relation between a item and a collection." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An organism that is a member of a population of organisms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is member of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "member part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "lbl" : "has member", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004096", + "lbl" : "DEPRECATED inheres in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004097", + "lbl" : "DEPRECATED bearer of", + "type" : "PROPERTY", + "meta" : { + "deprecated" : true + } + } ], + "edges" : [ { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000006", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000141" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000015", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000016", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000017", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000019", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000020", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000023", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000034", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000016" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000040", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000141", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000079", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000080", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000081", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000085", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000053" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000086", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000053" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000087", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000053" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000091", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000053" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000092", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000052" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002350", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002351", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000050", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000054", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/BFO_0000066", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000067" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000052", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000053" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000056", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000057" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000058", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000059" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000079", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000085" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000080", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000086" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000081", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000087" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0000091", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0000092" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0001000", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0001001" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0001015", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0001025" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002000", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002002" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002350", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002351" + } ], + "domainRangeAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000054", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000055", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000056", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000058", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000059", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000031" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000079", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000085", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000034" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000087", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000091", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000016" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002002", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000040" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000141" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0000086", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000019" ] + } ], + "propertyChainAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/BFO_0000066" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] + } ] + } ] +} \ No newline at end of file diff --git a/core.obo b/core.obo new file mode 100644 index 00000000..df6a5d10 --- /dev/null +++ b/core.obo @@ -0,0 +1,441 @@ +format-version: 1.2 +data-version: ro/releases/2023-02-19/core.owl +ontology: ro/core +property_value: http://purl.org/dc/elements/1.1/license https://creativecommons.org/publicdomain/zero/1.0/ +property_value: http://xmlns.com/foaf/0.1/homepage "https://github.com/oborel/obo-relations/wiki/ROCore" xsd:anyURI +property_value: owl:versionInfo "2023-02-19" xsd:string + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +disjoint_from: BFO:0000003 ! occurrent + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant + +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +is_a: BFO:0000003 ! occurrent + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + +[Term] +id: BFO:0000017 +name: realizable entity +def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant + +[Term] +id: BFO:0000023 +name: role +def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] +is_a: BFO:0000017 ! realizable entity + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] +is_a: BFO:0000002 ! continuant + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant +disjoint_from: BFO:0000141 ! immaterial entity + +[Term] +id: BFO:0000141 +name: immaterial entity +is_a: BFO:0000004 ! independent continuant + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true + +[Typedef] +id: BFO:0000054 +name: realized in +comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realized in" xsd:string +property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string +property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string +property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string +property_value: IAO:0000118 "is realized by" xsd:string +property_value: IAO:0000118 "realized_in" xsd:string +property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +inverse_of: BFO:0000055 ! realizes + +[Typedef] +id: BFO:0000055 +name: realizes +comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realizes" xsd:string +property_value: IAO:0000112 "this disease course realizes this disease" xsd:string +property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string +property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string +property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +domain: BFO:0000015 ! process +range: BFO:0000017 ! realizable entity + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000050 BFO:0000066 +inverse_of: BFO:0000067 ! contains process +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Typedef] +id: RO:0000052 +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +inverse_of: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000053 +name: has characteristic +def: "Inverse of characteristic_of" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant +is_inverse_functional: true + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: RO:0000079 +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 ! function +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000085 ! has function + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000085 +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000034 ! function +is_a: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! has characteristic +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +is_a: RO:0000052 ! characteristic of + +[Typedef] +id: RO:0001000 +name: derives from +def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string +property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string +property_value: IAO:0000118 "derives_from" xsd:string +inverse_of: RO:0001001 ! derives into + +[Typedef] +id: RO:0001001 +name: derives into +def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string +property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string +property_value: IAO:0000118 "derives_into" xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000111 "is location of" xsd:string +property_value: IAO:0000112 "my head is the location of my brain" xsd:string +property_value: IAO:0000112 "this cage is the location of this rat" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000118 "location_of" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string +property_value: IAO:0000111 "located in" xsd:string +property_value: IAO:0000112 "my brain is located in my head" xsd:string +property_value: IAO:0000112 "this rat is located in this cage" xsd:string +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000118 "located_in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true + +[Typedef] +id: RO:0002000 +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000050 ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0004096 +name: DEPRECATED inheres in +comment: DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. +is_obsolete: true + +[Typedef] +id: RO:0004097 +name: DEPRECATED bearer of +is_obsolete: true + diff --git a/core.owl b/core.owl index 227ebb83..31e29698 100644 --- a/core.owl +++ b/core.owl @@ -1,6 +1,6 @@ - + xmlns:terms="http://purl.org/dc/terms/"> - - + + 2023-02-19 https://github.com/oborel/obo-relations/wiki/ROCore @@ -50,6 +50,12 @@ + + + + + + @@ -80,9 +86,9 @@ - + - + @@ -92,6 +98,12 @@ + + + + + + @@ -635,27 +647,153 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + + - + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + - + - + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + spatial region + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + + disposition + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + + + + + + quality + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + generically dependent continuant + + + + + + + + + function + + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + immaterial entity + @@ -849,5 +987,5 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + diff --git a/el-constraints.owl b/el-constraints.owl deleted file mode 100644 index be5809d0..00000000 --- a/el-constraints.owl +++ /dev/null @@ -1,92 +0,0 @@ - - - - - - - - - - -]> - - - - - This ontology is intended for encoding constraints on ro/core in a way that is usable by EL reasoners such as Elk. In future this ontology may be derived by some automatic or semi-automatic translation process from a more direct encoding. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/generated-axioms.owl b/generated-axioms.owl deleted file mode 100644 index 4adb7c15..00000000 --- a/generated-axioms.owl +++ /dev/null @@ -1,152 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/go-biotic.owl b/go-biotic.owl deleted file mode 100644 index 8b2ae6ca..00000000 --- a/go-biotic.owl +++ /dev/null @@ -1,15 +0,0 @@ - - - - - - - - - diff --git a/go_cc_import.owl b/go_cc_import.owl deleted file mode 100644 index e98e6ad5..00000000 --- a/go_cc_import.owl +++ /dev/null @@ -1,165 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nucleus - - - - - - - - - biological_process - - - - - - - - - - membrane - - - - - - - - - - axon - - - - - - - - - - dendrite - - - - - - - - - - - presynaptic membrane - - - - - - - - - cell projection - - - - - - - - - - neuron projection - - - - - - - - - synapse part - - - - - - - - - - synapse - - - - - - - - - - - postsynaptic membrane - - - - - - - diff --git a/go_mf_import.owl b/go_mf_import.owl deleted file mode 100644 index 1f81d784..00000000 --- a/go_mf_import.owl +++ /dev/null @@ -1,116 +0,0 @@ - - - - - - - - - - - - - - - molecular_function - - - - - - - - catalytic activity - - - - - - - - - ubiquitin-protein ligase activity - - - - - - - - - kinase activity - - - - - - - - - transferase activity - - - - - - - - - transferase activity, transferring phosphorus-containing groups - - - - - - - - - ligase activity - - - - - - - - - ligase activity, forming carbon-nitrogen bonds - - - - - - - - - acid-amino acid ligase activity - - - - - - - - - small conjugating protein ligase activity - - - - - - - - - diff --git a/issue_template.md b/issue_template.md new file mode 100644 index 00000000..ac4497ce --- /dev/null +++ b/issue_template.md @@ -0,0 +1,21 @@ +For new term requests, please provide the following information: + +## Preferred term label + +(e.g., Asplenia) + +## Synonyms + +(e.g., Absent spleen) + +## Textual definition + +the definition should be understandable even for non-specialists. Include a PubMed ID to refer to any relevant article that provides additional information about the suggested term. + +## Suggested parent term + +Please look in the hierarchy in a browser such as [OLS](http://www.ebi.ac.uk/ols/ontologies/ro) + +## Attribution + +If you would like a nanoattribution, please indicate your ORCID id \ No newline at end of file diff --git a/pato_import.owl b/pato_import.owl deleted file mode 100644 index 7bad5f16..00000000 --- a/pato_import.owl +++ /dev/null @@ -1,93 +0,0 @@ - - - - - - - - - - - - - - - - - quality - - - - - - - - morphology - - - - - - - - - shape - - - - - - - - - structure - - - - - - - - - linear - - - - - - - - - physical object quality - - - - - - - - - laminar - - - - - - - - - - diff --git a/ro-base.json b/ro-base.json index 19f07664..69deb094 100644 --- a/ro-base.json +++ b/ro-base.json @@ -1,1430 +1,1353 @@ { "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/ro-base.json", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/description", + "val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." + }, { + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "OBO Relations Ontology" + }, { + "pred" : "http://purl.org/dc/elements/1.1/type", + "val" : "http://purl.obolibrary.org/obo/IAO_8000001" + }, { + "pred" : "http://purl.org/dc/terms/license", + "val" : "https://creativecommons.org/publicdomain/zero/1.0/" + }, { + "pred" : "http://www.w3.org/2002/07/owl#versionInfo", + "val" : "2023-02-19" + }, { + "pred" : "http://xmlns.com/foaf/0.1/homepage", + "val" : " https://github.com/oborel/obo-relations/" + } ], + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-19/ro-base.json" + }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "lbl" : "continuant", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" - } ] - }, - "type" : "PROPERTY", - "lbl" : "connected to" + "val" : "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002291", + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "lbl" : "occurrent", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." - } ] - }, - "type" : "PROPERTY", - "lbl" : "ubiquitously expressed in" + "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "lbl" : "independent continuant", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Inverse of 'expressed in'", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "PROPERTY", - "lbl" : "expresses" + "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002171", + "id" : "http://purl.obolibrary.org/obo/BFO_0000006", + "lbl" : "spatial region", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "lbl" : "process", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "non-overlapping with" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "shares no parts with" - }, { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX owl: \nPREFIX part_of: \nPREFIX mutually_spatially_disjoint_with: \nCONSTRUCT {\n part_of: a owl:ObjectProperty .\n [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?x ;\n owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?y\n ]\n ]\n}\nWHERE {\n ?x mutually_spatially_disjoint_with: ?y .\n}" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/RO_0002163" - } ] - }, - "type" : "PROPERTY", - "lbl" : "mutually spatially disjoint with" + "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015006", + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "lbl" : "disposition", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "lbl" : "realizable entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." } - }, - "type" : "PROPERTY", - "lbl" : "different in magnitude relative to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015007", + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "lbl" : "quality", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "lbl" : "specifically dependent continuant", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] - }, - "type" : "PROPERTY", - "lbl" : "increased in magnitude relative to" + "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "lbl" : "role", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] - }, - "type" : "PROPERTY", - "lbl" : "decreased in magnitude relative to" + "val" : "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015009", + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "lbl" : "generically dependent continuant", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." } - }, - "type" : "PROPERTY", - "lbl" : "similar in magnitude relative to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "lbl" : "function", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "lbl" : "material entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.", - "xrefs" : [ ] + "val" : "a core relation that holds between a part and its whole" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The M8 connects Glasgow and Edinburgh" + "val" : "my brain is part of my body (continuant parthood, two material entities)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" } ] - }, - "type" : "PROPERTY", - "lbl" : "connects" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + "val" : "this year has part this day (occurrent parthood)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in formation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realized in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + "val" : "this disease is realized in this disease course" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + "val" : "this fragility is realized in this shattering" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is realized in this investigation" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is realized by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "realized_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in morphogenesis of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", - "meta" : { - "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", "type" : "PROPERTY", - "lbl" : "attached to part of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002299", "meta" : { - "definition" : { - "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realizes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + "val" : "this disease course realizes this disease" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation realizes this investigator role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + "val" : "this shattering realizes this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000060", + "lbl" : "obsolete preceded by", "type" : "PROPERTY", - "lbl" : "results in maturation of" + "meta" : { + "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.", - "xrefs" : [ ] + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] - }, - "type" : "PROPERTY", - "lbl" : "supplies" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.", - "xrefs" : [ ] + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" } ] - }, - "type" : "PROPERTY", - "lbl" : "drains" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002172", + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.", - "xrefs" : [ ] + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occurs_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] - }, - "type" : "PROPERTY", - "lbl" : "taxonomic class assertion" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002293", + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of ubiquiotously expressed in", - "xrefs" : [ ] + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "site of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] - }, - "type" : "PROPERTY", - "lbl" : "ubiquitously expresses" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002173", + "id" : "http://purl.obolibrary.org/obo/BFO_0000141", + "lbl" : "immaterial entity", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - }, - "type" : "PROPERTY", - "lbl" : "ambiguous for taxon" + "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002174", + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.", - "xrefs" : [ ] + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." }, - "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "dubious for taxon" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).", - "xrefs" : [ ] + "val" : "Inverse of characteristic_of" }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in developmental progression of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.", - "xrefs" : [ ] + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + "val" : "this blood clot participates in this blood coagulation" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in development of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S", - "xrefs" : [ ] + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" }, - "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" }, { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - } ] - }, - "type" : "PROPERTY", - "lbl" : "present in taxon" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015015", - "meta" : { - "definition" : { - "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" + "val" : "this process has participant this input material (or this output material)" }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] - }, - "type" : "PROPERTY", - "lbl" : "has high plasma membrane amount" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "lbl" : "is concretized as", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", - "xrefs" : [ "PMID:19243617" ] + "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has low plasma membrane amount" - }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:05:45Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." } ] - }, - "type" : "PROPERTY", - "lbl" : "valid_for_gocam" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "lbl" : "concretizes", "type" : "PROPERTY", - "lbl" : "has relative magnitude" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015011", "meta" : { "definition" : { - "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." }, - "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] - }, - "type" : "PROPERTY", - "lbl" : "has cross section" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015012", - "meta" : { - "definition" : { - "val" : "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "comments" : [ "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality." ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", "type" : "PROPERTY", - "lbl" : "reciprocal of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002160", "meta" : { "definition" : { - "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.", - "xrefs" : [ ] + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + "val" : "this catalysis function is a function of this enzyme" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" } ] - }, - "type" : "PROPERTY", - "lbl" : "only in taxon" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Inverse of developmentally preceded by", - "xrefs" : [ ] + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "PROPERTY", - "lbl" : "developmentally succeeded by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002287", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" } ] - }, - "type" : "PROPERTY", - "lbl" : "part of developmental precursor of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.", - "xrefs" : [ ] + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - }, { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" } ] - }, - "type" : "PROPERTY", - "lbl" : "never in taxon" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.", - "xrefs" : [ ] + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" }, - "comments" : [ "Connects a biological entity to its taxon of origin." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9227-417X" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" } ] - }, - "type" : "PROPERTY", - "lbl" : "in taxon" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common", - "xrefs" : [ ] + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" } ] - }, - "type" : "PROPERTY", - "lbl" : "spatially disjoint from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else", - "xrefs" : [ ] + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "replaces" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", "type" : "PROPERTY", - "lbl" : "developmentally replaces" + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.", - "xrefs" : [ ] + "val" : "inverse of has disposition" }, - "comments" : [ "VBO calls this homologous_to" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "PROPERTY", - "lbl" : "shares ancestor with" + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "id" : "http://purl.obolibrary.org/obo/RO_0000300", + "lbl" : "obsolete in neural circuit with", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons." + }, + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "PROPERTY", - "lbl" : "serially homologous to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0019501", - "meta" : { - "definition" : { - "val" : "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" - } ] - }, - "type" : "PROPERTY", - "lbl" : "confers susceptibility to condition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000092", - "meta" : { - "definition" : { - "val" : "inverse of has disposition", - "xrefs" : [ ] - }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "disposition of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000091", - "meta" : { - "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0000301", + "lbl" : "obsolete upstream in neural circuit with", "type" : "PROPERTY", - "lbl" : "has disposition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003002", "meta" : { "definition" : { - "val" : "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.", - "xrefs" : [ ] + "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first." }, + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - } ] - }, - "type" : "PROPERTY", - "lbl" : "represses expression of" + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "id" : "http://purl.obolibrary.org/obo/RO_0000302", + "lbl" : "obsolete downstream in neural circuit with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a produced_by b iff some process that occurs_in b has_output a.", - "xrefs" : [ ] + "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - } ] - }, - "type" : "PROPERTY", - "lbl" : "produced by" + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.", - "xrefs" : [ ] + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "evolutionarily_descended_from" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this cell derives from this parent cell (cell division)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ancestral_stucture_of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this nucleus derives from this parent nucleus (nuclear division)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." } ] - }, - "type" : "PROPERTY", - "lbl" : "derived by descent from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003003", - "meta" : { - "definition" : { - "val" : "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", "type" : "PROPERTY", - "lbl" : "increases expression of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002157", "meta" : { "definition" : { - "val" : "inverse of derived by descent from", - "xrefs" : [ ] + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent cell derives into this cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent nucleus derives into this nucleus (nuclear division)" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_into" } ] - }, - "type" : "PROPERTY", - "lbl" : "has derived by descendant" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "X continuous_with Y if and only if X and Y share a fiat boundary.", - "xrefs" : [ ] + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is location of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my head is the location of my brain" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this cage is the location of this rat" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "connected to" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "FMA:85972" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "location_of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "continuous with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "id" : "http://purl.obolibrary.org/obo/RO_0001018", + "lbl" : "contained in", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x", - "xrefs" : [ ] - }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "contained in" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "proper overlaps" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained_in" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "partially overlaps" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003000", + "id" : "http://purl.obolibrary.org/obo/RO_0001019", + "lbl" : "contains", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.", - "xrefs" : [ ] - }, - "comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "contains" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "produces" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-07T12:58:06Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", "type" : "PROPERTY", - "lbl" : "in register with" + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002029", + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.", - "xrefs" : [ "PMID:24138933", "Wikipedia:Infant_mortality" ] + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." }, - "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-05-22T16:43:28Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", "type" : "PROPERTY", - "lbl" : "has increased age-specific mortality rate" + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0016004", + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y.", - "xrefs" : [ ] + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "located in" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ExO:0000083" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is located in my head" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has exposure medium" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0016001", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this rat is located in this cage" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-11-05T17:30:14Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/478" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "located_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" } ] - }, - "type" : "PROPERTY", - "lbl" : "has phenotype or disease" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0016002", + "id" : "http://purl.obolibrary.org/obo/RO_0001900", + "lbl" : "temporal interpretation", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.", - "xrefs" : [ ] + "val" : "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-11-05T17:30:44Z" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/478" + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" } ] - }, - "type" : "PROPERTY", - "lbl" : "has disease" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "id" : "http://purl.obolibrary.org/obo/RO_0001901", + "lbl" : "axiom holds for all times", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "FMA:85994" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/2212" - } ] - }, - "type" : "PROPERTY", - "lbl" : "branching part of" + "val" : "## Elucidation\n\nThis is used when the statement/axiom is assumed to hold true 'eternally'\n\n## How to interpret (informal)\n\nFirst the "atemporal" FOL is derived from the OWL using the standard\ninterpretation. This axiom is temporalized by embedding the axiom\nwithin a for-all-times quantified sentence. The t argument is added to\nall instantiation predicates and predicates that use this relation.\n\n## Example\n\n Class: nucleus\n SubClassOf: part_of some cell\n\n forall t :\n forall n :\n instance_of(n,Nucleus,t)\n implies\n exists c :\n instance_of(c,Cell,t)\n part_of(n,c,t)\n\n## Notes\n\nThis interpretation is *not* the same as an at-all-times relation" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "id" : "http://purl.obolibrary.org/obo/RO_0001902", + "lbl" : "relation has no temporal argument", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "## Elucidation\n\nThis is used when the first-order logic form of the relation is\nbinary, and takes no temporal argument.\n\n## Example:\n\n Class: limb\n SubClassOf: develops_from some lateral-plate-mesoderm\n\n forall t, t2:\n forall x :\n instance_of(x,Limb,t)\n implies\n exists y :\n instance_of(y,LPM,t2)\n develops_from(x,y)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence", - "xrefs" : [ ] + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this investigator role is a role of this person" + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is role of" + "val" : "2D_boundary_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "role_of" + "val" : "boundary of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "role of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "id" : "http://purl.obolibrary.org/obo/RO_0002001", + "lbl" : "aligned with", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence", - "xrefs" : [ ] - }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "quality_of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A quality inheres in its bearer at all times for which the quality exists." + "val" : "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is quality of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this red color is a quality of this apple" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "quality of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence", - "xrefs" : [ ] + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_function" + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_2D_boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "has function" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "lbl" : "electrically_synapsed_to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.", - "xrefs" : [ ] + "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "affects", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "acts upstream of or within" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "id" : "http://purl.obolibrary.org/obo/RO_0002004", + "lbl" : "tracheates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y", - "xrefs" : [ ] + "val" : "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] - }, - "type" : "PROPERTY", - "lbl" : "has potential to developmentally contribute to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "id" : "http://purl.obolibrary.org/obo/RO_0002005", + "lbl" : "innervated_by", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:24Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", "type" : "PROPERTY", - "lbl" : "directly regulated by" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y", - "xrefs" : [ ] + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] - }, - "type" : "PROPERTY", - "lbl" : "has potential to developmentally induce" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "lbl" : "coincident with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." }, + "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:38Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note from NCEAS meeting: consider changing primary label" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly negatively regulated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "id" : "http://purl.obolibrary.org/obo/RO_0002009", + "lbl" : "cell expresses", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "val" : "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:47Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.org/dc/terms/description", + "val" : "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly positively regulated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "lbl" : "regulates in other organism", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y", - "xrefs" : [ ] + "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] - }, - "type" : "PROPERTY", - "lbl" : "has potential to develop into" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "id" : "http://purl.obolibrary.org/obo/RO_0002011", + "lbl" : "regulates transport of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y", - "xrefs" : [ ] + "val" : "A relationship that holds between a process that regulates a transport process and the entity transported by that process." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] - }, - "type" : "PROPERTY", - "lbl" : "has potential to directly develop into" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "lbl" : "occurrent part of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] + "val" : "A part of relation that applies only between occurrents." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." }, - "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-22T14:14:36Z" + "val" : "2017-05-24T09:30:46Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has effector activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path.", - "xrefs" : [ ] + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/2212" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "main stem of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002260", - "meta" : { - "definition" : { - "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", "type" : "PROPERTY", - "lbl" : "has biological role" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002382", "meta" : { "definition" : { - "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y", - "xrefs" : [ ] + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "proper distributary of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002261", - "meta" : { - "definition" : { - "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "lbl" : "has necessary component activity", "type" : "PROPERTY", - "lbl" : "has application role" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000087", "meta" : { - "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence", - "xrefs" : [ ] - }, + "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has role" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.", - "xrefs" : [ ] - }, + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-07-20T17:11:08Z" + "val" : "2017-05-24T09:44:33Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "transports" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002262", - "meta" : { - "definition" : { - "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", "type" : "PROPERTY", - "lbl" : "has chemical role" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002383", "meta" : { "definition" : { - "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y", - "xrefs" : [ ] + "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "proper tributary of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "lbl" : "has ligand", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence", - "xrefs" : [ ] + "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this apple has quality this red color" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_quality" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-19T17:30:36Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has quality" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "lbl" : "transports", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).", - "xrefs" : [ ] + "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:11:08Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has developmental potential involving" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.", - "xrefs" : [ ] + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", @@ -1433,6723 +1356,6039 @@ "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-07-20T17:19:37Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "occurs across" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "acts upstream of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.", - "xrefs" : [ ] + "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", + "xrefs" : [ "GOC:dos" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-07-19T17:30:36Z" + "val" : "2017-09-17T13:52:38Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has ligand" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence", - "xrefs" : [ ] + "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this catalysis function is a function of this enzyme" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "function_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is function of" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "function of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.", - "xrefs" : [ ] + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "anastomoses with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "anabranch of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.", - "xrefs" : [ ] + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] }, - "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:31:17Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has positive regulatory component activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "id" : "http://purl.obolibrary.org/obo/RO_0002029", + "lbl" : "has increased age-specific mortality rate", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Inverse of developmentally induced by", - "xrefs" : [ ] + "val" : "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.", + "xrefs" : [ "PMID:24138933", "Wikipedia:Infant_mortality" ] }, + "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T16:43:28Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "developmentally induces" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p", - "xrefs" : [ ] - }, - "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + "val" : "David Osumi-Sutherland" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" } ] - }, - "type" : "PROPERTY", - "lbl" : "developmentally preceded by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x spatially_coextensive_with y if and inly if x and y have the same location", - "xrefs" : [ ] - }, + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A lump of clay and a statue" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "spatially coextensive with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", "meta" : { - "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:36:08Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "has necessary component activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", "meta" : { - "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:44:33Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "has component activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", "type" : "PROPERTY", - "lbl" : "defined by inverse" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002018", "meta" : { - "definition" : { - "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.", - "xrefs" : [ ] - }, + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:49:21Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "di" } ] - }, - "type" : "PROPERTY", - "lbl" : "has component process" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))", - "xrefs" : [ ] - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "existence overlaps" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002374", + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat", - "xrefs" : [ ] - }, - "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "has fused element", - "xrefs" : [ ] - } ], + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "David Osumi-Sutherland" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "false" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" } ] - }, - "type" : "PROPERTY", - "lbl" : "derived from ancestral fusion of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "lbl" : "during which starts", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t", - "xrefs" : [ ] - }, + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002494" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "immediate transformation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002011", + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A relationship that holds between a process that regulates a transport process and the entity transported by that process.", - "xrefs" : [ ] - }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "regulates transport of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.", - "xrefs" : [ ] - }, + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has fasciculating component" + "val" : "meets" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" } ] - }, - "type" : "PROPERTY", - "lbl" : "has fasciculating neuron projection" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "inverse of connecting branch of", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" } ] - }, - "type" : "PROPERTY", - "lbl" : "has connecting branch" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.", - "xrefs" : [ ] - }, + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/170" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. 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The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "existence ends during or before" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "id" : "http://purl.obolibrary.org/obo/RO_0002105", + "lbl" : "synapsed_via_type_Ib_bouton_to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.", - "xrefs" : [ ] + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton." }, + "comments" : [ "Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:30:46Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "has regulatory component activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "id" : "http://purl.obolibrary.org/obo/RO_0002106", + "lbl" : "synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has developmental contribution from", - "xrefs" : [ ] + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "developmentally contributes to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "id" : "http://purl.obolibrary.org/obo/RO_0002107", + "lbl" : "synapsed_via_type_II_bouton_to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. 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For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "comments" : [ "Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:31:01Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "has negative regulatory component activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "id" : "http://purl.obolibrary.org/obo/RO_0002108", + "lbl" : "synapsed_by_via_type_II_bouton", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T", - "xrefs" : [ ] + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type II bouton." }, + "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0001-5948-3092" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO:0001759" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002109", + "lbl" : "synapsed_by_via_type_Ib_bouton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton." + }, + "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "https://orcid.org/0000-0001-5948-3092" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "induced by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We place this under 'developmentally preceded by'. 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" }, - "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. 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The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n\t and some (\n\t http://purl.obolibrary.org/obo/GO_0042734 and some (\n\t and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "existence ends with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "id" : "http://purl.obolibrary.org/obo/RO_0002130", + "lbl" : "has synaptic terminal in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y", - "xrefs" : [ ] + "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + "val" : " some ( that some Y?)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "overlaps" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "lbl" : "overlaps", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. 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CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "transformation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "id" : "http://purl.obolibrary.org/obo/RO_0002134", + "lbl" : "innervates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.", - "xrefs" : [ ] + "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/2212" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that ( some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "connecting branch of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).", - "xrefs" : [ ] + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" } ] - }, - "type" : "PROPERTY", - "lbl" : "regulates in other organism" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.", - "xrefs" : [ ] + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" }, - "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note from NCEAS meeting: consider changing primary label" + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "coincident with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002009", + "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "lbl" : "derived by descent from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.", - "xrefs" : [ ] + "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/description", - "val" : "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral_stucture_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "evolutionarily_descended_from" } ] - }, - "type" : "PROPERTY", - "lbl" : "cell expresses" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002004", + "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "lbl" : "has derived by descendant", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).", - "xrefs" : [ ] + "val" : "inverse of derived by descent from" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] - }, - "type" : "PROPERTY", - "lbl" : "tracheates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).", - "xrefs" : [ ] + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, + "comments" : [ "VBO calls this homologous_to" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" } ] - }, - "type" : "PROPERTY", - "lbl" : "existence starts during" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002246", - "meta" : { - "definition" : { - "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "lbl" : "serially homologous to", "type" : "PROPERTY", - "lbl" : "under-expressed in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002005", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] - }, - "type" : "PROPERTY", - "lbl" : "innervated_by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).", - "xrefs" : [ ] + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "existence starts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.", - "xrefs" : [ ] + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "has active pharmaceutical ingredient", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "has active substance", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Any portion of roundup 'has active ingredient' some glyphosate" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has active ingredient" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002006", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "has synaptic terminal of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000", - "xrefs" : [ ] + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." }, - "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "https://orcid.org/0000-0001-9227-417X" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "bounding layer of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002249", - "meta" : { - "definition" : { - "val" : "inverse of has active ingredient", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", "type" : "PROPERTY", - "lbl" : "active ingredient in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002000", "meta" : { "definition" : { - "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity", - "xrefs" : [ ] + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the surface of my skin is a 2D boundary of my body" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is 2D boundary of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is boundary of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "boundary of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "2D_boundary_of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "surface of" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", "type" : "PROPERTY", - "lbl" : "2D boundary of" + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002121", + "id" : "http://purl.obolibrary.org/obo/RO_0002171", + "lbl" : "mutually spatially disjoint with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n\t", - "xrefs" : [ ] + "val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "non-overlapping with" }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no parts with" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some (\n\t and some (\n\t http://purl.obolibrary.org/obo/GO_0042734 and some (\n\t and some ?Y)))" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX owl: \nPREFIX part_of: \nPREFIX mutually_spatially_disjoint_with: \nCONSTRUCT {\n part_of: a owl:ObjectProperty .\n [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?x ;\n owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?y\n ]\n ]\n}\nWHERE {\n ?x mutually_spatially_disjoint_with: ?y .\n}" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/RO_0002163" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" } ] - }, - "type" : "PROPERTY", - "lbl" : "dendrite synapsed in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "id" : "http://purl.obolibrary.org/obo/RO_0002172", + "lbl" : "taxonomic class assertion", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor", - "xrefs" : [ ] + "val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ExO:0000055" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "has exposure route" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002484", + "id" : "http://purl.obolibrary.org/obo/RO_0002173", + "lbl" : "ambiguous for taxon", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "curator guidance link" + "val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "id" : "http://purl.obolibrary.org/obo/RO_0002174", + "lbl" : "dubious for taxon", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T." + }, + "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See notes for inverse relation" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "receives input from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002001", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", "type" : "PROPERTY", - "lbl" : "aligned with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002243", "meta" : { "definition" : { - "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target.", - "xrefs" : [ ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "has exposure transport path" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity", - "xrefs" : [ ] + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_2D_boundary" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has 2D boundary the surface of my skin" + "val" : "The M8 connects Glasgow and Edinburgh" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has boundary" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] - }, - "type" : "PROPERTY", - "lbl" : "has 2D boundary" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002486", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", "type" : "PROPERTY", - "lbl" : "sends output to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002244", "meta" : { "definition" : { - "val" : "Any relationship between an exposure event or process and any other entity.", - "xrefs" : [ ] + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" } ] - }, - "type" : "PROPERTY", - "lbl" : "related via exposure to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" } ] - }, - "type" : "PROPERTY", - "lbl" : "relation between physical entity and a process or stage" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions.", - "xrefs" : [ ] + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" } ] - }, - "type" : "PROPERTY", - "lbl" : "electrically_synapsed_to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002245", - "meta" : { - "definition" : { - "val" : "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", "type" : "PROPERTY", - "lbl" : "over-expressed in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002480", "meta" : { "definition" : { - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y", - "xrefs" : [ ] + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Axiomatization to GO to be added later" + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ] - }, - "type" : "PROPERTY", - "lbl" : "ubiquitinates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002481", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", "type" : "PROPERTY", - "lbl" : "is kinase activity" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002360", "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has dendrite location" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.", - "xrefs" : [ ] + "val" : "inverse of has phenotype" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ExO:0000001" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has exposure receptor" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002482", - "meta" : { - "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is ubiquitination" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002120", + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n ", - "xrefs" : [ ] + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], + "comments" : [ "This is the transitive form of the develops from relation" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that part_of some ( that some ( that some Y?)))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "val" : "https://orcid.org/0000-0001-9114-8737" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.", - "xrefs" : [ ] + "val" : "inverse of develops from" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ExO:0000000" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" } ] - }, - "type" : "PROPERTY", - "lbl" : "has exposure stressor" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002483", + "id" : "http://purl.obolibrary.org/obo/RO_0002204", + "lbl" : "gene product of", "type" : "PROPERTY", - "lbl" : "inherited annotation property" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000059", "meta" : { "definition" : { - "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.", - "xrefs" : [ ] + "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "concretizes" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "lbl" : "has gene product", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.", - "xrefs" : [ ] + "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is concretized as" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process", - "xrefs" : [ ] + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this process has participant this input material (or this output material)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this blood coagulation has participant this blood clot" + "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_participant" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this investigation has participant this investigator" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has participant" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has participant" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002356", + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. ", - "xrefs" : [ ] + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", "type" : "PROPERTY", - "lbl" : "results in specification of" + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002114", + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a motor neuron and a muscle that it synapses to via a type III bouton.", - "xrefs" : [ ] + "val" : "inverse of parasitoid of" }, - "comments" : [ "Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed_via_type_III_bouton_to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location", - "xrefs" : [ ] + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "located in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "located_in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is located in my head" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this rat is located in this cage" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" } ] - }, - "type" : "PROPERTY", - "lbl" : "located in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.", - "xrefs" : [ ] + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] - }, - "type" : "PROPERTY", - "lbl" : "capable of positively regulating" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002235", - "meta" : { - "definition" : { - "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", "type" : "PROPERTY", - "lbl" : "stem parasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002477", "meta" : { "definition" : { - "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism", - "xrefs" : [ ] + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "child nucleus of in hermaphrodite" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002115", - "meta" : { - "definition" : { - "val" : "Relation between a muscle and a motor neuron that synapses to it via a type III bouton.\n", - "xrefs" : [ ] - }, - "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed_by_via_type_III_bouton" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "id" : "http://purl.obolibrary.org/obo/RO_0002214", + "lbl" : "has prototype", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A child nucleus relationship in which the cells are part of a male organism", - "xrefs" : [ ] + "val" : "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "child nucleus of in male" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.", - "xrefs" : [ ] + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in developmental induction of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002599", - "meta" : { - "definition" : { - "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "treats" + "val" : "has function realized in" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pazopanib -> pathological angiogenesis" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." } ] - }, - "type" : "PROPERTY", - "lbl" : "capable of inhibiting or preventing pathological process" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002236", - "meta" : { - "definition" : { - "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", "type" : "PROPERTY", - "lbl" : "root parasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002479", "meta" : { "definition" : { - "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.", - "xrefs" : [ ] + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] - }, - "type" : "PROPERTY", - "lbl" : "has part that occurs in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002237", - "meta" : { - "definition" : { - "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002217", + "lbl" : "obsolete actively participates in", "type" : "PROPERTY", - "lbl" : "hemiparasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002238", "meta" : { "definition" : { - "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys.", - "xrefs" : [ ] + "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" }, + "comments" : [ "Obsoleted as the inverse property was obsoleted." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." - } ] - }, - "type" : "PROPERTY", - "lbl" : "has component participant" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "agent in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002608" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0017001", + "id" : "http://purl.obolibrary.org/obo/RO_0002218", + "lbl" : "obsolete has active participant", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.", - "xrefs" : [ ] + "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "utilizes", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A diagnostic testing device utilizes a specimen." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has agent" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-11-08T12:00:00Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "device utilizes material" + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002500" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y", - "xrefs" : [ ] + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts with process that occurs in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "has start location" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.", - "xrefs" : [ ] + "val" : "x adjacent to y if and only if x and y share a boundary." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "composed primarily of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002110", + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. ", - "xrefs" : [ ] + "val" : "inverse of surrounded by" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapsed in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "has postsynaptic terminal in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.", - "xrefs" : [ ] - }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this red color is a characteristic of this apple" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this fragility is a characteristic of this vase" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres_in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "inheres in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" } ] - }, - "type" : "PROPERTY", - "lbl" : "characteristic of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001021", - "meta" : { - "definition" : { - "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "is autoimmune trigger for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002594", - "meta" : { - "definition" : { - "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", "type" : "PROPERTY", - "lbl" : "is relational form of a class" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002352", "meta" : { "definition" : { - "val" : "inverse of has input", - "xrefs" : [ ] + "val" : "inverse of starts with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Allen" } ] - }, - "type" : "PROPERTY", - "lbl" : "input of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y", - "xrefs" : [ ] + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends with process that occurs in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has end location" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002111", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has neurotransmitter" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" } ] - }, - "type" : "PROPERTY", - "lbl" : "releases neurotransmitter" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.", - "xrefs" : [ ] + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] - }, - "type" : "PROPERTY", - "lbl" : "causal relation between material entity and a process" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has output", - "xrefs" : [ ] + "val" : "x develops_in y if x is located in y whilst x is developing" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" } ] - }, - "type" : "PROPERTY", - "lbl" : "output of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has allergic trigger" + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002474", + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. 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}, - "type" : "PROPERTY", - "lbl" : "capable of regulating" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002475", + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.", - "xrefs" : [ ] + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "shares no connection with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - 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"pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that some ( that some Y?)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapses in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "val" : "consumes" } ] - }, - "type" : "PROPERTY", - "lbl" : "has presynaptic terminal in" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.", - "xrefs" : [ ] + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "produces" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", "type" : "PROPERTY", - "lbl" : "has output" + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d", - "xrefs" : [ ] + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0001-9625-1899" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." } ] - }, - "type" : "PROPERTY", - "lbl" : "child nucleus of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.", - "xrefs" : [ ] + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "val" : "ExO:0000001" } ] - }, - "type" : "PROPERTY", - "lbl" : "capable of negatively regulating" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002355", + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.", - "xrefs" : [ ] + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in structural organization of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process", - "xrefs" : [ ] + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this investigator participates in this investigation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this input material (or this output material) participates in this process" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this blood clot participates in this blood coagulation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "participates in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "participates_in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" } ] - }, - "type" : "PROPERTY", - "lbl" : "participates in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002590", + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", "type" : "PROPERTY", - "lbl" : "results in disassembly of" + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is subject of eating interaction with" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002245", + "lbl" : "over-expressed in", "type" : "PROPERTY", - "lbl" : "eats" + "meta" : { + "definition" : { + "val" : "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002591", + "id" : "http://purl.obolibrary.org/obo/RO_0002246", + "lbl" : "under-expressed in", "type" : "PROPERTY", - "lbl" : "results in remodeling of" + "meta" : { + "definition" : { + "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "is member of is a mereological relation between a item and a collection.", - "xrefs" : [ ] + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is member of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "member part of" + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An organism that is a member of a population of organisms" + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", "type" : "PROPERTY", - "lbl" : "member of" + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "eaten by" + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is target of eating interaction with" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] - }, - "type" : "PROPERTY", - "lbl" : "is eaten by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002592", + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "results in organization of" + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002472", + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b.", - "xrefs" : [ ] + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is evidence for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of", - "xrefs" : [ ] + "val" : "inverse of has developmental contribution from" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this apple is bearer of this red color" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this vase is bearer of this fragility" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is bearer of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "bearer_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "bearer of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has characteristic" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", - "xrefs" : [ ] + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" } ] - }, - "type" : "PROPERTY", - "lbl" : "ends with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.", - "xrefs" : [ ] + "val" : "Inverse of developmentally induced by" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is allergic trigger for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "has member is a mereological relation between a collection and an item.", - "xrefs" : [ ] + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "lbl" : "defined by inverse", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", "type" : "PROPERTY", - "lbl" : "has member" + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002593", + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y).", - "xrefs" : [ ] + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" } - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", "type" : "PROPERTY", - "lbl" : "existence ends at start of" + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002349", + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.", - "xrefs" : [ ] + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in determination of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002228", - "meta" : { - "definition" : { - "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", "type" : "PROPERTY", - "lbl" : "facultative parasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002107", "meta" : { "definition" : { - "val" : "A relation between a motor neuron and a muscle that it synapses to via a type II bouton.", - "xrefs" : [ ] + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." }, - "comments" : [ "Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-5948-3092" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed_via_type_II_bouton_to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001018", + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contained_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "contained in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" + "val" : "replaces" } ] - }, - "type" : "PROPERTY", - "lbl" : "contained in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001019", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "contains" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", "type" : "PROPERTY", - "lbl" : "contains" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002229", "meta" : { "definition" : { - "val" : "inverse of ends with", - "xrefs" : [ ] + "val" : "Inverse of developmentally preceded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "ends" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002108", + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Relation between a muscle and a motor neuron that synapses to it via a type II bouton.", - "xrefs" : [ ] - }, - "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-5948-3092" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed_by_via_type_II_bouton" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002109", + "id" : "http://purl.obolibrary.org/obo/RO_0002291", + "lbl" : "ubiquitously expressed in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.", - "xrefs" : [ ] + "val" : "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" }, - "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-5948-3092" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed_by_via_type_Ib_bouton" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. ", - "xrefs" : [ ] + "val" : "Inverse of 'expressed in'" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002224", - "meta" : { + "id" : "http://purl.obolibrary.org/obo/RO_0002293", + "lbl" : "ubiquitously expresses", + "type" : "PROPERTY", + "meta" : { "definition" : { - "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", - "xrefs" : [ ] + "val" : "inverse of ubiquiotously expressed in" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "starts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002466", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", "type" : "PROPERTY", - "lbl" : "is commensalism" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002345", "meta" : { "definition" : { - "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.", - "xrefs" : [ ] + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" } ] - }, - "type" : "PROPERTY", - "lbl" : "exports" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002587", - "type" : "PROPERTY", - "lbl" : "results in synthesis of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002588", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", "type" : "PROPERTY", - "lbl" : "results in assembly of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002104", "meta" : { "definition" : { - "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.", - "xrefs" : [ ] + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1617-8244" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( and some ?Y)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9990-8331" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" } ] - }, - "type" : "PROPERTY", - "lbl" : "has plasma membrane part" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y", - "xrefs" : [ ] + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - 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}, - "type" : "PROPERTY", - "lbl" : "location of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002467", + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" } ] - }, - "type" : "PROPERTY", - "lbl" : "is mutualism" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x develops_in y if x is located in y whilst x is developing", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Jonathan Bard, EHDAA2" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "EHDAA2" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" } ] - }, - "type" : "PROPERTY", - "lbl" : "develops in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002589", + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "results in catabolism of" + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002105", + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton.", - "xrefs" : [ ] + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." }, - "comments" : [ "Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - 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"val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed_via_type_Ib_bouton_to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002468", + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - 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"pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in commitment to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002106", + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton.", - "xrefs" : [ ] + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." }, - 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The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:55:39Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/173" } ] - }, - "type" : "PROPERTY", - "lbl" : "provides nutrients for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002227", - "meta" : { - "definition" : { - "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002312", + "lbl" : "evolutionary variant of", "type" : "PROPERTY", - "lbl" : "obligate parasite of" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:04:12Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" } ] - }, - "type" : "PROPERTY", - "lbl" : "valid_for_go_ontology" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x adjacent to y if and only if x and y share a boundary.", - "xrefs" : [ ] + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation acts as a join point with BSPO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] - }, - "type" : "PROPERTY", - "lbl" : "adjacent to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l ", - "xrefs" : [ ] + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in transport along" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002462", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" } ] - }, - "type" : "PROPERTY", - "lbl" : "subject participant in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002583", - "meta" : { - "definition" : { - "val" : "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y).", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "existence starts at end of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003310", - "meta" : { - "definition" : { - "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", "type" : "PROPERTY", - "lbl" : "condition ameliorated by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002584", "meta" : { "definition" : { - "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p", - "xrefs" : [ ] + "val" : "A relationship that holds via some environmental process" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." } ] - }, - "type" : "PROPERTY", - "lbl" : "has part structure that is capable of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of surrounded by", - "xrefs" : [ ] + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" } ] - }, - "type" : "PROPERTY", - "lbl" : "surrounds" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" } ] - }, - "type" : "PROPERTY", - "lbl" : "target participant in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and an anatomical structure that its soma is part of.", - "xrefs" : [ ] + "val" : "A mereological relationship or a topological relationship" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some (\n and some ?Y)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "has soma location" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.", - "xrefs" : [ ] + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in transport across" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n", - "xrefs" : [ ] + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "fasciculates with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "PROPERTY", - "lbl" : "fasciculates with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002222", - "meta" : { - "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" } ] - }, - "type" : "PROPERTY", - "lbl" : "temporally related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " } ] - }, - "type" : "PROPERTY", - "lbl" : "results in growth of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002464", + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." } ] - }, - "type" : "PROPERTY", - "lbl" : "helper property (not for use in curation)" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002585", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in closure of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002586", - "meta" : { - "definition" : { - "val" : "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", "type" : "PROPERTY", - "lbl" : "results in breakdown of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002102", "meta" : { "definition" : { - "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in.", - "xrefs" : [ ] + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" } ] - }, - "type" : "PROPERTY", - "lbl" : "axon synapses in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of starts with", - "xrefs" : [ ] + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" } ] - }, - "type" : "PROPERTY", - "lbl" : "starts" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in transport to from or in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003311", - "meta" : { - "definition" : { - "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", "type" : "PROPERTY", - "lbl" : "condition exacerbated by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002465", "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" } ] - }, - "type" : "PROPERTY", - "lbl" : "is symbiosis" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002580", + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", "type" : "PROPERTY", - "lbl" : "logical macro assertion on an axiom" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002460", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" } ] - }, - "type" : "PROPERTY", - "lbl" : "has vector" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", "type" : "PROPERTY", - "lbl" : "is a defining property chain axiom" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002461", "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" } ] - }, - "type" : "PROPERTY", - "lbl" : "partner in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.", - "xrefs" : [ ] + "val" : "inverse of regulates" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" } ] - }, - "type" : "PROPERTY", - "lbl" : "imports" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", "type" : "PROPERTY", - "lbl" : "is a defining property chain axiom where second argument is reflexive" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003307", "meta" : { "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.", - "xrefs" : [ ] + "val" : "inverse of negatively regulates" }, - "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preventative for condition" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "ameliorates condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Anopheles is a vector for Plasmodium" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is vector for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002217", + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role", - "xrefs" : [ ] + "val" : "A relationship that holds via some process of localization" }, - "comments" : [ "Obsoleted as the inverse property was obsoleted." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "agent in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0002608" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete actively participates in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.", - "xrefs" : [ ] + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has target start location" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.", - "xrefs" : [ ] + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has target end location" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002218", + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y", - "xrefs" : [ ] + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has agent" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0002500" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete has active participant" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003306", - "meta" : { - "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contributes to penetrance of condition" } ] - }, - "type" : "PROPERTY", - "lbl" : "contributes to frequency of condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x", - "xrefs" : [ ] + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "surrounded by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003309", - "meta" : { - "definition" : { - "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "exacerbates condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003308", - "meta" : { - "definition" : { - "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", "type" : "PROPERTY", - "lbl" : "correlated with condition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002334", "meta" : { "definition" : { - "val" : "inverse of regulates", - "xrefs" : [ ] + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" } ] - }, - "type" : "PROPERTY", - "lbl" : "regulated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "positively regulates (process to process)" } ] - }, - "type" : "PROPERTY", - "lbl" : "positively regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003303", - "meta" : { - "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", "type" : "PROPERTY", - "lbl" : "causes condition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002576", "meta" : { - "definition" : { - "val" : "inverse of has skeleton", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "skeleton of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002455", + "id" : "http://purl.obolibrary.org/obo/RO_0002345", + "lbl" : "exports", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is subject of pollination interaction with" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/pollinates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Bees pollinate Flowers" } ] - }, - "type" : "PROPERTY", - "lbl" : "pollinates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "id" : "http://purl.obolibrary.org/obo/RO_0002348", + "lbl" : "results in commitment to", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has polinator" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is target of pollination interaction with" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/hasPollinator" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "pollinated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "id" : "http://purl.obolibrary.org/obo/RO_0002349", + "lbl" : "results in determination of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of negatively regulates", - "xrefs" : [ ] + "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "negatively regulated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "lbl" : "member of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.", - "xrefs" : [ ] + "val" : "is member of is a mereological relation between a item and a collection." }, - "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + "val" : "An organism that is a member of a population of organisms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is member of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "member part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "causes or contributes to condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002577", + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "lbl" : "has member", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A material entity consisting of multiple components that are causally integrated.", - "xrefs" : [ ] + "val" : "has member is a mereological relation between a collection and an item." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.jbiomedsem.com/content/4/1/43" + "val" : "SIO" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "CLASS", - "lbl" : "system" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002214", + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "lbl" : "input of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation.", - "xrefs" : [ ] + "val" : "inverse of has input" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO: add homeomorphy axiom" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" } ] - }, - "type" : "PROPERTY", - "lbl" : "has prototype" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "lbl" : "output of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q.", - "xrefs" : [ ] + "val" : "inverse of has output" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly regulates (processual)" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "lbl" : "formed as result of", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "acquires nutrients from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "id" : "http://purl.obolibrary.org/obo/RO_0002355", + "lbl" : "results in structural organization of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of positively regulates", - "xrefs" : [ ] + "val" : "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "positively regulated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "id" : "http://purl.obolibrary.org/obo/RO_0002356", + "lbl" : "results in specification of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ", - "xrefs" : [ ] + "val" : "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" } ] - }, - "type" : "PROPERTY", - "lbl" : "capable of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.", - "xrefs" : [ ] + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contributes to expressivity of condition" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "contributes to severity of condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002579", + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" - }, { - "pred" : "http://purl.org/dc/terms/creator", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" } ] - }, - "type" : "PROPERTY", - "lbl" : "is indirect form of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003304", - "meta" : { - "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", "type" : "PROPERTY", - "lbl" : "contributes to condition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002458", "meta" : { "definition" : { - "val" : "inverse of preys on", - "xrefs" : [ ] + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/HasPredator" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is target of predation interaction with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has predator" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" } ] - }, - "type" : "PROPERTY", - "lbl" : "preyed upon by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds via some process of localization", - "xrefs" : [ ] + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" } ] - }, - "type" : "PROPERTY", - "lbl" : "related via localization to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.", - "xrefs" : [ ] + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + "val" : "http://dbpedia.org/property/insertion" } ] - }, - "type" : "PROPERTY", - "lbl" : "capable of part of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002451", + "id" : "http://purl.obolibrary.org/obo/RO_0002374", + "lbl" : "derived from ancestral fusion of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between a disease and organism", - "xrefs" : [ ] + "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" }, + "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "has fused element" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "all dengue disease transmitted by some mosquito" + "val" : "false" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Add domain and range constraints" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" } ] - }, - "type" : "PROPERTY", - "lbl" : "transmitted by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002572", - "meta" : { - "definition" : { - "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", "type" : "PROPERTY", - "lbl" : "luminal space of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002330", "meta" : { "definition" : { - "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.", - "xrefs" : [ ] + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" } ] - }, - "type" : "PROPERTY", - "lbl" : "genomically related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", - "xrefs" : [ ] + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this nucleus derives from this parent nucleus (nuclear division)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + "val" : "Deschutes River tributary_of Columbia River" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this cell derives from this parent cell (cell division)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." + "val" : "inferior epigastric vein tributary_of external iliac vein" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "derives_from" - } ] - }, - "type" : "PROPERTY", - "lbl" : "derives from" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002331", - "meta" : { - "definition" : { - "val" : "c involved_in p if and only if c enables some process p', and p' is part of p", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { + "val" : "drains into" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enables part of" + "val" : "drains to" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "actively involved in" + "val" : "tributary channel of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" - } ] - }, - "type" : "PROPERTY", - "lbl" : "involved in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002210", - "meta" : { - "definition" : { - "val" : "inverse of directly develops from", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "developmental precursor of" + "val" : "http://dbpedia.org/ontology/drainsTo" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly develops into" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002573", + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between an attribute or a qualifier and another attribute.", - "xrefs" : [ ] + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" } ] - }, - "type" : "PROPERTY", - "lbl" : "has modifier" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002452", + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between a disease or an organism and a phenotype", - "xrefs" : [ ] + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" } ] - }, - "type" : "PROPERTY", - "lbl" : "has symptom" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002574", + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" } ] - }, - "type" : "PROPERTY", - "lbl" : "participates in a biotic-biotic interaction with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.", - "xrefs" : [ ] + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7476-6306" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-3837-8864" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" } ] - }, - "type" : "PROPERTY", - "lbl" : "regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", - "xrefs" : [ ] + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this parent cell derives into this cell (cell division)" + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this parent nucleus derives into this nucleus (nuclear division)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "derives_into" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] - }, - "type" : "PROPERTY", - "lbl" : "derives into" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002453", + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "host of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", - "xrefs" : [ ] + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" }, - "comments" : [ "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-1048-5019" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is used to study" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has role in modeling" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c", - "xrefs" : [ ] + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "regulates levels of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y", - "xrefs" : [ ] + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/hasHost" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has host" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.", - "xrefs" : [ ] + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] - }, - "type" : "PROPERTY", - "lbl" : "negatively regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of enables", - "xrefs" : [ ] + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "enabled by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002575", + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y", - "xrefs" : [ ] + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002423", - "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://purl.org/dc/terms/creator", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "is direct form of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0040042", + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.", - "xrefs" : [ ] + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." }, - "comments" : [ "R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-10-21T19:46:34Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/164" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "part-of is homeomorphic for independent continuants." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002401", + "lbl" : "obsolete has indirect input", "type" : "PROPERTY", - "lbl" : "is homeomorphic for" + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "id" : "http://purl.obolibrary.org/obo/RO_0002402", + "lbl" : "obsolete has direct output", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.", - "xrefs" : [ ] + "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "translation SubClassOf has_direct_output some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "UBERON:cjm" - } ] - }, - "type" : "PROPERTY", - "lbl" : "conduit for" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly produces" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002571", + "id" : "http://purl.obolibrary.org/obo/RO_0002403", + "lbl" : "obsolete has indirect output", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "lumen of" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.", - "xrefs" : [ ] + "val" : "inverse of upstream of" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "molecularly increases activity of", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly activates" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly positively regulates activity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "molecularly controls", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002406", + "lbl" : "obsolete directly activates", "type" : "PROPERTY", - "lbl" : "directly regulates activity of" + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002629" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002569", + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of branching part of", - "xrefs" : [ ] + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002408", + "lbl" : "obsolete directly inhibits", "type" : "PROPERTY", - "lbl" : "has branching part" + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002630" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process", - "xrefs" : [ ] + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" } ] - }, - "type" : "PROPERTY", - "lbl" : "expressed in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c enables p iff c is capable of p and c acts to execute p.", - "xrefs" : [ ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "catalyzes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is catalyzing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is executing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", "type" : "PROPERTY", - "lbl" : "enables" + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.", - "xrefs" : [ ] + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." }, - "comments" : [ "TODO - add child relations from DOS" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "has developmental precursor", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" + "val" : "http://purl.obolibrary.org/obo/RO_0002411" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly develops from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.", - "xrefs" : [ ] + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "molecularly decreases activity of", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" + "val" : "directly provides input for" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly negatively regulates activity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.", - "xrefs" : [ ] + "val" : "transitive form of directly_provides_input_for" }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" } ] - }, - "type" : "PROPERTY", - "lbl" : "functionally related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "id" : "http://purl.obolibrary.org/obo/RO_0002416", + "lbl" : "logical macro assertion", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p.", - "xrefs" : [ ] + "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "part of structure that is capable of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002208", - "meta" : { - "definition" : { - "val" : "A parasite that kills or sterilizes its host", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "parasitoid of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002209", - "meta" : { - "definition" : { - "val" : "inverse of parasitoid of", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", "type" : "PROPERTY", - "lbl" : "has parasitoid" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002323", "meta" : { "definition" : { - "val" : "A mereological relationship or a topological relationship", - "xrefs" : [ ] + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "mereotopologically related to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002444", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "direct parasite of", - "xrefs" : [ ] + "pred" : "hasRelatedSynonym", + "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Pediculus humanus capitis parasite of human" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "parasitizes" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/parasitizes" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002419", + "lbl" : "annotation property cardinality", "type" : "PROPERTY", - "lbl" : "parasite of" + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "id" : "http://purl.obolibrary.org/obo/RO_0002420", + "lbl" : "logical macro assertion on a class", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", - "xrefs" : [ ] + "val" : "A logical macro assertion whose domain is an IRI for a class" }, - "comments" : [ "This is the transitive form of the develops from relation" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002421", + "lbl" : "logical macro assertion on a property", "type" : "PROPERTY", - "lbl" : "develops from" + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a property" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002565", + "id" : "http://purl.obolibrary.org/obo/RO_0002422", + "lbl" : "logical macro assertion on an object property", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "lbl" : "logical macro assertion on an annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002424", + "lbl" : "differs in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This is an exploratory relation" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in movement of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "id" : "http://purl.obolibrary.org/obo/RO_0002425", + "lbl" : "differs in attribute of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "inverse of develops from", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "develops into" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002445", + "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "lbl" : "differs in attribute", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "directly parasitized by", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has parasite" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/hasParasite" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "parasitised by" } ] - }, - "type" : "PROPERTY", - "lbl" : "parasitized by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).", - "xrefs" : [ ] + "val" : "inverse of causally upstream of or within" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally influences" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)", - "xrefs" : [ ] + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" } ] - }, - "type" : "PROPERTY", - "lbl" : "developmentally related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between elements of a musculoskeletal system or its analogs.", - "xrefs" : [ ] + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] - }, - "type" : "PROPERTY", - "lbl" : "biomechanically related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].", - "xrefs" : [ ] + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] - }, - "type" : "PROPERTY", - "lbl" : "colocalizes with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002204", + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"", - "xrefs" : [ ] + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." + "val" : "OWL does not allow defining object properties via a Union" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" } ] - }, - "type" : "PROPERTY", - "lbl" : "gene product of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.", - "xrefs" : [ ] + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "semibiotically interacts with", - "xrefs" : [ ] + "pred" : "hasExactSynonym", + "val" : "enables activity in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Porifiera attaches to substrate" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" } ] - }, - "type" : "PROPERTY", - "lbl" : "participates in a abiotic-biotic interaction with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y", - "xrefs" : [ ] + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" } ] - }, - "type" : "PROPERTY", - "lbl" : "has gene product" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] - }, - "type" : "PROPERTY", - "lbl" : "contributes to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002568", - "meta" : { - "definition" : { - "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Antagonist_(muscle)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", "type" : "PROPERTY", - "lbl" : "has muscle antagonist" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002447", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000316" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0208" } ] - }, - "type" : "PROPERTY", - "lbl" : "phosphorylates" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "lbl" : "molecularly interacts with", "type" : "PROPERTY", - "lbl" : "definition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018002", "meta" : { "definition" : { - "val" : "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input", - "xrefs" : [ ] + "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/conformsTo", - "val" : "http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "binds" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "molecularly binds with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] - }, - "type" : "PROPERTY", - "lbl" : "myristoylates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018001", + "id" : "http://purl.obolibrary.org/obo/RO_0002437", + "lbl" : "biotically interacts with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Helper relation for OWL definition of RO:0018002 myristoylates", - "xrefs" : [ ] + "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "interacts with on organism level" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/interactsWith" } ] - }, - "type" : "PROPERTY", - "lbl" : "is myristoyltransferase activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018003", + "id" : "http://purl.obolibrary.org/obo/RO_0002438", + "lbl" : "trophically interacts with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of myristoylates", - "xrefs" : [ ] + "val" : "An interaction relationship in which the partners are related via a feeding relationship." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - }, - "type" : "PROPERTY", - "lbl" : "myristoylated by" - }, { - "id" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "is defined by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0002000", - "meta" : { - "definition" : { - "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "lbl" : "preys on", "type" : "PROPERTY", - "lbl" : "defined by construct" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0040035", "meta" : { "definition" : { - "val" : "This relation groups relations between diseases and any other kind of entity.", - "xrefs" : [ ] + "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Baleen whale preys on krill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7134-3324" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-3138-4118" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-09-26T00:00:32Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of predation interaction with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preys upon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/preysUpon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.inaturalist.org/observations/2942824" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease relationship" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002440", + "lbl" : "symbiotically interacts with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A biotic interaction in which the two organisms live together in more or less intimate association.", - "xrefs" : [ ] + "val" : "A biotic interaction in which the two organisms live together in more or less intimate association." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" } ] - }, - "type" : "PROPERTY", - "lbl" : "symbiotically interacts with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002561", - "meta" : { - "definition" : { - "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is symmetric relational form of process class" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002441", + "lbl" : "commensually interacts with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).", - "xrefs" : [ ] + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" } ] - }, - "type" : "PROPERTY", - "lbl" : "commensually interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "id" : "http://purl.obolibrary.org/obo/RO_0002442", + "lbl" : "mutualistically interacts with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds via some environmental process", - "xrefs" : [ ] + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" } ] - }, - "type" : "PROPERTY", - "lbl" : "evolutionarily related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002562", - "meta" : { - "definition" : { - "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "lbl" : "interacts with via parasite-host interaction", "type" : "PROPERTY", - "lbl" : "is relational form of process class" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0040036", "meta" : { "definition" : { - "val" : "p has anatomical participant c iff p has participant c, and c is an anatomical entity", - "xrefs" : [ ] + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-09-26T01:08:58Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in changes to anatomical or cellular structure" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "id" : "http://purl.obolibrary.org/obo/RO_0002444", + "lbl" : "parasite of", + "type" : "PROPERTY", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "direct parasite of" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Pediculus humanus capitis parasite of human" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitizes" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + "val" : "http://eol.org/schema/terms/parasitizes" } ] - }, - "type" : "PROPERTY", - "lbl" : "interaction relation helper property" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "id" : "http://purl.obolibrary.org/obo/RO_0002445", + "lbl" : "parasitized by", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)", - "xrefs" : [ ] - }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "directly parasitized by" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" - } ] - }, - "type" : "PROPERTY", - "lbl" : "ecologically related to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002200", - "meta" : { - "definition" : { - "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" } ] - }, - "type" : "PROPERTY", - "lbl" : "has phenotype" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002442", + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).", - "xrefs" : [ ] + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "semibiotically interacts with" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Porifiera attaches to substrate" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" } ] - }, - "type" : "PROPERTY", - "lbl" : "mutualistically interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "id" : "http://purl.obolibrary.org/obo/RO_0002447", + "lbl" : "phosphorylates", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "adapted for" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] - }, - "type" : "PROPERTY", - "lbl" : "confers advantage in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "lbl" : "directly regulates activity of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has phenotype", - "xrefs" : [ ] + "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" } ] - }, - "type" : "PROPERTY", - "lbl" : "phenotype of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).", - "xrefs" : [ ] + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly decreases activity of" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly inhibits" } ] - }, - "type" : "PROPERTY", - "lbl" : "interacts with via parasite-host interaction" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "lbl" : "directly positively regulates activity of", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly increases activity of" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly activates" } ] - }, - "type" : "PROPERTY", - "lbl" : "molecular interaction relation helper property" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002560", + "id" : "http://purl.obolibrary.org/obo/RO_0002451", + "lbl" : "transmitted by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p", - "xrefs" : [ ] + "val" : "A relationship that holds between a disease and organism" }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "all dengue disease transmitted by some mosquito" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Add domain and range constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is asymmetric relational form of process class" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002558", + "id" : "http://purl.obolibrary.org/obo/RO_0002452", + "lbl" : "has symptom", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of is evidence for", - "xrefs" : [ ] + "val" : "A relation that holds between a disease or an organism and a phenotype" }, - "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/25052702" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has evidence" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002437", + "id" : "http://purl.obolibrary.org/obo/RO_0002453", + "lbl" : "host of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.", - "xrefs" : [ ] - }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/interactsWith" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "interacts with on organism level" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" } ] - }, - "type" : "PROPERTY", - "lbl" : "biotically interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002438", + "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "lbl" : "has host", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship in which the partners are related via a feeding relationship.", - "xrefs" : [ ] + "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasHost" } ] - }, - "type" : "PROPERTY", - "lbl" : "trophically interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "id" : "http://purl.obolibrary.org/obo/RO_0002455", + "lbl" : "pollinates", + "type" : "PROPERTY", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Bees pollinate Flowers" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of pollination interaction with" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influenced by (entity-centric)" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/pollinates" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally influenced by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "lbl" : "pollinated by", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members", - "xrefs" : [ ] - }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Baleen whale preys on krill" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/preysUpon" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preys upon" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is subject of predation interaction with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7134-3324" + "val" : "has polinator" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-3138-4118" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of pollination interaction with" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.inaturalist.org/observations/2942824" + "val" : "http://eol.org/schema/terms/hasPollinator" } ] - }, - "type" : "PROPERTY", - "lbl" : "preys on" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "lbl" : "acquires nutrients from", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.", - "xrefs" : [ ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." } ] - }, - "type" : "PROPERTY", - "lbl" : "contributes to morphology of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "id" : "http://purl.obolibrary.org/obo/RO_0002458", + "lbl" : "preyed upon by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of hyperparasite of", - "xrefs" : [ ] + "val" : "inverse of preys on" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "has epiparasite", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "has hyperparasite", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "hyperparasitoidized by", - "xrefs" : [ ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "hyperparasitized by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002312", - "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "evolutionary variant of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002434", - "meta" : { - "definition" : { - "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "in pairwise interaction with", - "xrefs" : [ ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0914" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has predator" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of predation interaction with" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/HasPredator" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Considering relabeling as 'pairwise interacts with'" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" } ] - }, - "type" : "PROPERTY", - "lbl" : "interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002555", + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "lbl" : "is vector for", + "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Allelopathy" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/allelopathyYes" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" } ] - }, - "type" : "PROPERTY", - "lbl" : "allelopath of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "id" : "http://purl.obolibrary.org/obo/RO_0002460", + "lbl" : "has vector", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "regulates localization of" } ] - }, - "type" : "PROPERTY", - "lbl" : "transports or maintains localization of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "id" : "http://purl.obolibrary.org/obo/RO_0002461", + "lbl" : "partner in", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" } ] - }, - "type" : "PROPERTY", - "lbl" : "characteristic of part of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002556", + "id" : "http://purl.obolibrary.org/obo/RO_0002462", + "lbl" : "subject participant in", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." } ] - }, - "type" : "PROPERTY", - "lbl" : "pathogen of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0208" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ECO_0000316" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." } ] - }, - "type" : "PROPERTY", - "lbl" : "genetically interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "id" : "http://purl.obolibrary.org/obo/RO_0002464", + "lbl" : "helper property (not for use in curation)", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." } ] - }, - "type" : "PROPERTY", - "lbl" : "molecularly interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "id" : "http://purl.obolibrary.org/obo/RO_0002465", + "lbl" : "is symbiosis", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in acquisition of features of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002557", + "id" : "http://purl.obolibrary.org/obo/RO_0002466", + "lbl" : "is commensalism", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has pathogen" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002550", + "id" : "http://purl.obolibrary.org/obo/RO_0002467", + "lbl" : "is mutualism", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "end, weeks post birth" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002551", + "id" : "http://purl.obolibrary.org/obo/RO_0002468", + "lbl" : "is parasitism", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has supporting framework" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." } ] - }, - "type" : "PROPERTY", - "lbl" : "has skeleton" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p", - "xrefs" : [ ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] - }, - "type" : "PROPERTY", - "lbl" : "involved in negative regulation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002310", + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.", - "xrefs" : [ ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," - }, { - "pred" : "http://purl.org/dc/terms/creator", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-06-05T17:55:39Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/pull/173" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" } ] - }, - "type" : "CLASS", - "lbl" : "exposure event or process" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p", - "xrefs" : [ ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "OWL does not allow defining object properties via a Union" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" } ] - }, - "type" : "PROPERTY", - "lbl" : "involved in or involved in regulation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002552", + "id" : "http://purl.obolibrary.org/obo/RO_0002472", + "lbl" : "is evidence for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.", - "xrefs" : [ ] + "val" : "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in ending of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002553", + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y", - "xrefs" : [ ] + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "epiparasite of", - "xrefs" : [ ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "hyperparasitoid of", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Hyperparasite" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://eol.org/schema/terms/hyperparasitoidOf" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002474", + "lbl" : "dispositional interpretation", "type" : "PROPERTY", - "lbl" : "hyperparasite of" + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "id" : "http://purl.obolibrary.org/obo/RO_0002475", + "lbl" : "has no connections with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other." }, - "comments" : [ "" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "enables activity in", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes activity in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A protein that enables activity in a cytosol." + "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no connection with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" } ] - }, - "type" : "PROPERTY", - "lbl" : "is active in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.", - "xrefs" : [ ] + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/creator", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." } ] - }, - "type" : "PROPERTY", - "lbl" : "causally upstream of, negative effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002547", + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Count of number of days intervening between the start of the stage and the time of coitum.", - "xrefs" : [ ] + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "start, days post coitum" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "differs in attribute" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of causally upstream of or within", - "xrefs" : [ ] + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally downstream of or within" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002548", + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Count of number of days intervening between the end of the stage and the time of coitum.", - "xrefs" : [ ] + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "end, days post coitum" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002549", + "id" : "http://purl.obolibrary.org/obo/RO_0002481", + "lbl" : "is kinase activity", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "start, weeks post birth" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "id" : "http://purl.obolibrary.org/obo/RO_0002482", + "lbl" : "is ubiquitination", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "involved in regulation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "id" : "http://purl.obolibrary.org/obo/RO_0002483", + "lbl" : "inherited annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002484", + "lbl" : "curator guidance link", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p", - "xrefs" : [ ] - }, + "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "involved in positive regulation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002543", + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "start, months post birth" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "May be merged into parent relation" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." } ] - }, - "type" : "PROPERTY", - "lbl" : "results in developmental regression of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002422", - "meta" : { - "definition" : { - "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", "type" : "PROPERTY", - "lbl" : "logical macro assertion on an object property" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002302", "meta" : { "definition" : { - "val" : "Inverse of 'is substance that treats'", - "xrefs" : [ ] + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/creator", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is treated by substance" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", "type" : "PROPERTY", - "lbl" : "logical macro assertion on an annotation property" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002544", "meta" : { "definition" : { - "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2", - "xrefs" : [ ] + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" - } ] - }, - "type" : "PROPERTY", - "lbl" : "end, months post birth" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002424", - "meta" : { - "comments" : [ "This is an exploratory relation" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "false" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" } ] - }, - "type" : "PROPERTY", - "lbl" : "differs in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs.", - "xrefs" : [ ] + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-4366-3088" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "adapted for living in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has habitat" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002545", + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.", - "xrefs" : [ ] + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "exists during" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "month of gestation" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.", - "xrefs" : [ ] + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, - "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/creator", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally upstream of, positive effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002546", + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process", - "xrefs" : [ ] + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has developmental stage marker" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002425", + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "differs in attribute of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018028", + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level", - "xrefs" : [ ] + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "https://orcid.org/0000-0003-4423-4370" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://www.wikidata.org/wiki/Property:P9275" + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" } ] - }, - "type" : "PROPERTY", - "lbl" : "is inverse agonist of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018027", - "meta" : { - "definition" : { - "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "https://orcid.org/0000-0003-4423-4370" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://www.wikidata.org/wiki/Property:P3772" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", "type" : "PROPERTY", - "lbl" : "is agonist of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018029", "meta" : { "definition" : { - "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level", - "xrefs" : [ ] + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "https://orcid.org/0000-0003-4423-4370" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://www.wikidata.org/wiki/Property:P3773" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is antagonist of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.", - "xrefs" : [ ] + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-06-05T17:35:04Z" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6996-0040" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-8461-9745" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has exposure stimulus" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002540", - "meta" : { - "definition" : { - "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", "type" : "PROPERTY", - "lbl" : "end, days post fertilization" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002420", "meta" : { "definition" : { - "val" : "A logical macro assertion whose domain is an IRI for a class", - "xrefs" : [ ] + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, - "type" : "PROPERTY", - "lbl" : "logical macro assertion on a class" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002541", - "meta" : { - "definition" : { - "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", "type" : "PROPERTY", - "lbl" : "start, years post birth" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002542", "meta" : { "definition" : { - "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2", - "xrefs" : [ ] + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" - } ] - }, - "type" : "PROPERTY", - "lbl" : "end, years post birth" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002300", - "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "May be merged into parent relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] - }, - "type" : "PROPERTY", - "lbl" : "results in disappearance of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002421", - "meta" : { - "definition" : { - "val" : "A logical macro assertion whose domain is an IRI for a property", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "logical macro assertion on a property" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002536", + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", "type" : "PROPERTY", - "lbl" : "measurement property has unit" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002537", "meta" : { "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] - }, - "type" : "PROPERTY", - "lbl" : "has start time value" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002416", - "meta" : { - "definition" : { - "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002503", + "lbl" : "towards", "type" : "PROPERTY", - "lbl" : "logical macro assertion" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0019001", "meta" : { "definition" : { - "val" : "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.", - "xrefs" : [ ] + "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" } ] - }, - "type" : "PROPERTY", - "lbl" : "positively regulates characteristic" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002538", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002504", + "lbl" : "always present in taxon", "type" : "PROPERTY", - "lbl" : "has end time value" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0019000", "meta" : { "definition" : { - "val" : "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.", - "xrefs" : [ ] + "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brain always_present_in_taxon 'Vertebrata'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "forelimb always_present_in_taxon Euarchontoglires" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "never lost in" } ] - }, - "type" : "PROPERTY", - "lbl" : "regulates characteristic" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "id" : "http://purl.obolibrary.org/obo/RO_0002505", + "lbl" : "has intermediate", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.", - "xrefs" : [ ] + "val" : "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "affects", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "influences (processual)" + "val" : "has intermediate product" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally upstream of or within" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002539", + "id" : "http://purl.obolibrary.org/obo/RO_0002506", + "lbl" : "causal relation between entities", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] - }, - "type" : "PROPERTY", - "lbl" : "start, days post fertilization" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "id" : "http://purl.obolibrary.org/obo/RO_0002507", + "lbl" : "determined by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.", - "xrefs" : [ ] + "val" : "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A coral reef environment is determined by a particular coral reef" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/24330602" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determined by (system to material entity)" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally upstream of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002532", + "id" : "http://purl.obolibrary.org/obo/RO_0002508", + "lbl" : "determines", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Any entity that is ordered in discrete units along a linear axis.", - "xrefs" : [ ] + "val" : "inverse of determined by" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determines (material entity to system)" } ] - }, - "type" : "CLASS", - "lbl" : "sequentially ordered entity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "id" : "http://purl.obolibrary.org/obo/RO_0002509", + "lbl" : "determined by part of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.", - "xrefs" : [ ] + "val" : "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" } ] - }, - "type" : "PROPERTY", - "lbl" : "immediately causally upstream of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002533", + "id" : "http://purl.obolibrary.org/obo/RO_0002510", + "lbl" : "transcribed from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Any individual unit of a collection of like units arranged in a linear order", - "xrefs" : [ ] + "val" : "x is transcribed from y if and only if x is synthesized from template y" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" } ] - }, - "type" : "CLASS", - "lbl" : "sequence atomic unit" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002534", + "id" : "http://purl.obolibrary.org/obo/RO_0002511", + "lbl" : "transcribed to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Any entity that can be divided into parts such that each part is an atomical unit of a sequence", - "xrefs" : [ ] + "val" : "inverse of transcribed from" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" } ] - }, - "type" : "CLASS", - "lbl" : "sequence bearer" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "id" : "http://purl.obolibrary.org/obo/RO_0002512", + "lbl" : "ribosomal translation of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.", - "xrefs" : [ ] + "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly provides input for (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly provides input for" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" } ] - }, - "type" : "PROPERTY", - "lbl" : "provides input for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "id" : "http://purl.obolibrary.org/obo/RO_0002513", + "lbl" : "ribosomally translates to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "transitive form of directly_provides_input_for", - "xrefs" : [ ] + "val" : "inverse of ribosomal translation of" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "transitively provides input for (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - } ] - }, - "type" : "PROPERTY", - "lbl" : "transitively provides input for" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002535", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" } ] - }, - "type" : "PROPERTY", - "lbl" : "temporal logical macro assertion on a class" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002419", - "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002514", + "lbl" : "sequentially related to", "type" : "PROPERTY", - "lbl" : "annotation property cardinality" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0019002", "meta" : { "definition" : { - "val" : "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.", - "xrefs" : [ ] + "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. " }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "negatively regulates characteristic" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000426", - "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002530", + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y", - "xrefs" : [ ] + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002529" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" + "val" : "Two consecutive DNA residues are sequentially adjacent" }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "is immediately downstream of sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002531", + "id" : "http://purl.obolibrary.org/obo/RO_0002516", + "lbl" : "has start sequence", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of immediately downstream of", - "xrefs" : [ ] + "val" : "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "is immediately upstream of sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + "val" : "inverse of has start sequence" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "id" : "http://purl.obolibrary.org/obo/RO_0002518", + "lbl" : "has end sequence", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of upstream of", - "xrefs" : [ ] + "val" : "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ended by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally downstream of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "id" : "http://purl.obolibrary.org/obo/RO_0002519", + "lbl" : "is end sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has subsequence", - "xrefs" : [ ] + "val" : "inverse of has end sequence" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contained by" + "val" : "ends" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is subsequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "id" : "http://purl.obolibrary.org/obo/RO_0002520", + "lbl" : "is consecutive sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y.", - "xrefs" : [ ] + "val" : "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the SO paper, this was defined as an instance-type relation" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "overlaps sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "id" : "http://purl.obolibrary.org/obo/RO_0002521", + "lbl" : "is sequentially aligned with", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "immediately causally downstream of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002527", + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "lbl" : "bounds sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y.", - "xrefs" : [ ] + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "disconnected from" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "does not overlap sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002406", - "meta" : { - "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0002629" - } ], - "deprecated" : true - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002523", + "lbl" : "is bound by sequence of", "type" : "PROPERTY", - "lbl" : "obsolete directly activates" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002407", "meta" : { "definition" : { - "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.", - "xrefs" : [ ] + "val" : "inverse of bounds sequence of" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002213" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "indirectly positively regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "lbl" : "has subsequence", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of downstream of sequence of", - "xrefs" : [ ] + "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is upstream of sequence of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contains" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002521", + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "lbl" : "is subsequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering", - "xrefs" : [ ] + "val" : "inverse of has subsequence" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained by" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is sequentially aligned with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "lbl" : "overlaps sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.", - "xrefs" : [ ] + "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly consumes" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "has direct input" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002401", + "id" : "http://purl.obolibrary.org/obo/RO_0002527", + "lbl" : "does not overlap sequence of", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "definition" : { + "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete has indirect input" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "disconnected from" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "lbl" : "is upstream of sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y", - "xrefs" : [ ] + "val" : "inverse of downstream of sequence of" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "bounds sequence of" + } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "lbl" : "is downstream of sequence of", "type" : "PROPERTY", - "lbl" : "in_subset" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002523", "meta" : { "definition" : { - "val" : "inverse of bounds sequence of", - "xrefs" : [ ] + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" @@ -8157,3092 +7396,2331 @@ "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "is bound by sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002402", + "id" : "http://purl.obolibrary.org/obo/RO_0002530", + "lbl" : "is immediately downstream of sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. ", - "xrefs" : [ ] + "val" : "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly produces" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "translation SubClassOf has_direct_output some protein" + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002529" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete has direct output" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "id" : "http://purl.obolibrary.org/obo/RO_0002531", + "lbl" : "is immediately upstream of sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x", - "xrefs" : [ ] + "val" : "inverse of immediately downstream of" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contains" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "has subsequence" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002403", + "id" : "http://purl.obolibrary.org/obo/RO_0002532", + "lbl" : "sequentially ordered entity", + "type" : "CLASS", "meta" : { - "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "definition" : { + "val" : "Any entity that is ordered in discrete units along a linear axis." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete has indirect output" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002408", - "meta" : { - "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0002630" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete directly inhibits" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "id" : "http://purl.obolibrary.org/obo/RO_0002533", + "lbl" : "sequence atomic unit", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y.", - "xrefs" : [ ] + "val" : "Any individual unit of a collection of like units arranged in a linear order" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." } ] - }, - "type" : "PROPERTY", - "lbl" : "is downstream of sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "id" : "http://purl.obolibrary.org/obo/RO_0002534", + "lbl" : "sequence bearer", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.", - "xrefs" : [ ] + "val" : "Any entity that can be divided into parts such that each part is an atomical unit of a sequence" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002212" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002535", + "lbl" : "temporal logical macro assertion on a class", "type" : "PROPERTY", - "lbl" : "indirectly negatively regulates" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002640", + "id" : "http://purl.obolibrary.org/obo/RO_0002536", + "lbl" : "measurement property has unit", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002537", + "lbl" : "has start time value", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A sub-relation of endoparasite-of in which the parasite inhabits host cells.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002538", + "lbl" : "has end time value", "type" : "PROPERTY", - "lbl" : "intracellular endoparasite of" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002520", + "id" : "http://purl.obolibrary.org/obo/RO_0002539", + "lbl" : "start, days post fertilization", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.", - "xrefs" : [ ] + "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "In the SO paper, this was defined as an instance-type relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "is consecutive sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002641", + "id" : "http://purl.obolibrary.org/obo/RO_0002540", + "lbl" : "end, days post fertilization", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of intracellular endoparasite of", - "xrefs" : [ ] + "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "has intracellular endoparasite" + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002514", + "id" : "http://purl.obolibrary.org/obo/RO_0002541", + "lbl" : "start, years post birth", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. ", - "xrefs" : [ ] + "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "sequentially related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002635", + "id" : "http://purl.obolibrary.org/obo/RO_0002542", + "lbl" : "end, years post birth", "type" : "PROPERTY", - "lbl" : "has endoparasite" + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "id" : "http://purl.obolibrary.org/obo/RO_0002543", + "lbl" : "start, months post birth", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y", - "xrefs" : [ ] + "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every UTR is adjacent to a CDS of the same transcript" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Two consecutive DNA residues are sequentially adjacent" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "sequentially adjacent to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002636", - "meta" : { - "definition" : { - "val" : "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002544", + "lbl" : "end, months post birth", "type" : "PROPERTY", - "lbl" : "mesoparasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002516", "meta" : { "definition" : { - "val" : "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence", - "xrefs" : [ ] + "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every CDS has as a start sequence the start codon for that transcript" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "has start sequence" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002637", - "meta" : { - "definition" : { - "val" : "inverse of mesoparasite of", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002545", + "lbl" : "month of gestation", "type" : "PROPERTY", - "lbl" : "has mesoparasite" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002638", "meta" : { "definition" : { - "val" : "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.", - "xrefs" : [ ] + "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "intercellular endoparasite of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "id" : "http://purl.obolibrary.org/obo/RO_0002546", + "lbl" : "has developmental stage marker", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has start sequence", - "xrefs" : [ ] + "val" : "A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "is start sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002510", + "id" : "http://purl.obolibrary.org/obo/RO_0002547", + "lbl" : "start, days post coitum", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is transcribed from y if and only if x is synthesized from template y", - "xrefs" : [ ] + "val" : "Count of number of days intervening between the start of the stage and the time of coitum." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "transcribed from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002511", + "id" : "http://purl.obolibrary.org/obo/RO_0002548", + "lbl" : "end, days post coitum", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of transcribed from", - "xrefs" : [ ] + "val" : "Count of number of days intervening between the end of the stage and the time of coitum." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "transcribed to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002632", + "id" : "http://purl.obolibrary.org/obo/RO_0002549", + "lbl" : "start, weeks post birth", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "ectoparasite of" + } }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "id" : "http://purl.obolibrary.org/obo/RO_0002550", + "lbl" : "end, weeks post birth", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:05:29Z" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "valid_for_go_annotation_extension" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002633", - "meta" : { - "definition" : { - "val" : "inverse of ectoparasite of", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002551", + "lbl" : "has skeleton", "type" : "PROPERTY", - "lbl" : "has ectoparasite" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002512", "meta" : { "definition" : { - "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y", - "xrefs" : [ ] + "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has supporting framework" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." } ] - }, - "type" : "PROPERTY", - "lbl" : "ribosomal translation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002513", + "id" : "http://purl.obolibrary.org/obo/RO_0002552", + "lbl" : "results in ending of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of ribosomal translation of", - "xrefs" : [ ] + "val" : "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "ribosomally translates to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002634", + "id" : "http://purl.obolibrary.org/obo/RO_0002553", + "lbl" : "hyperparasite of", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "hyperparasitoid of" + }, { "pred" : "hasRelatedSynonym", - "val" : "lives inside of", - "xrefs" : [ ] + "val" : "epiparasite of" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + "val" : "http://eol.org/schema/terms/hyperparasitoidOf" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" + "val" : "https://en.wikipedia.org/wiki/Hyperparasite" } ] - }, - "type" : "PROPERTY", - "lbl" : "endoparasite of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002518", + "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "lbl" : "hyperparasitized by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence", - "xrefs" : [ ] + "val" : "inverse of hyperparasite of" }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "has epiparasite" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ended by" + "pred" : "hasRelatedSynonym", + "val" : "has hyperparasite" }, { + "pred" : "hasRelatedSynonym", + "val" : "hyperparasitoidized by" + } ], + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - 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}, - "type" : "PROPERTY", - "lbl" : "directly negatively regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002503", + "id" : "http://purl.obolibrary.org/obo/RO_0002557", + "lbl" : "has pathogen", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2", - "xrefs" : [ ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "towards" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002624", + "id" : "http://purl.obolibrary.org/obo/RO_0002558", + "lbl" : "has evidence", "type" : "PROPERTY", - "lbl" : "lays eggs in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002504", "meta" : { "definition" : { - "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S", - "xrefs" : [ ] + "val" : "inverse of is evidence for" }, + "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very strong relation. 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A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "determines (material entity to system)" + "val" : "causally influences (entity-centric)" } ] - }, - "type" : "PROPERTY", - "lbl" : "determines" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002509", + "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "lbl" : "biomechanically related to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.", - "xrefs" : [ ] + "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." } ] - }, - "type" : "PROPERTY", - "lbl" : "determined by part of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002613", + "id" : "http://purl.obolibrary.org/obo/RO_0002568", + "lbl" : "has muscle antagonist", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom", - "xrefs" : [ ] + "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Antagonist_(muscle)" } ] - }, - "type" : "PROPERTY", - "lbl" : "axiom contradicted by evidence" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002614", + "id" : "http://purl.obolibrary.org/obo/RO_0002569", + "lbl" : "has branching part", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.", - "xrefs" : [ ] + "val" : "inverse of branching part of" }, - "comments" : [ "In the Gene Ontology association model, this corresponds to the With/From field" ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is evidence with support from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002615", - "meta" : { - "definition" : { - "val" : "Inverse of is-model-of", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "lbl" : "conduit for", "type" : "PROPERTY", - "lbl" : "has model" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002616", "meta" : { + "definition" : { + "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "UBERON:cjm" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." + "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." } ] - }, - "type" : "PROPERTY", - "lbl" : "related via evidence or inference to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002610", + "id" : "http://purl.obolibrary.org/obo/RO_0002571", + "lbl" : "lumen of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.", - "xrefs" : [ ] + "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Groups both positive and negative correlation" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:cjm" } ] - }, - "type" : "PROPERTY", - "lbl" : "correlated with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002611", + "id" : "http://purl.obolibrary.org/obo/RO_0002572", + "lbl" : "luminal space of", "type" : "PROPERTY", - "lbl" : "evidential logical macro assertion on an axiom" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002612", "meta" : { "definition" : { - "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom", - "xrefs" : [ ] + "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "axiom has evidence" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002617", + "id" : "http://purl.obolibrary.org/obo/RO_0002573", + "lbl" : "has modifier", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.", - "xrefs" : [ ] + "val" : "A relation that holds between an attribute or a qualifier and another attribute." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." } ] - }, - "type" : "PROPERTY", - "lbl" : "is representative IRI for equivalence set" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002618", + "id" : "http://purl.obolibrary.org/obo/RO_0002574", + "lbl" : "participates in a biotic-biotic interaction with", + "type" : "PROPERTY", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/74" + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" } ] - }, - "type" : "PROPERTY", - "lbl" : "visits" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002619", + "id" : "http://purl.obolibrary.org/obo/RO_0002575", + "lbl" : "is direct form of", "type" : "PROPERTY", - "lbl" : "visited by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009002", "meta" : { "definition" : { - "val" : "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.", - "xrefs" : [ ] + "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'egg white' 'has substance removed' some 'egg yolk'" + "pred" : "http://purl.obolibrary.org/obo/RO_0002423", + "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-8844-9165" + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "has substance removed" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009001", + "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "lbl" : "skeleton of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.", - "xrefs" : [ ] + "val" : "inverse of has skeleton" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-8844-9165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "muffin 'has substance added' some 'baking soda'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has substance added" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000028", + "id" : "http://purl.obolibrary.org/obo/RO_0002577", + "lbl" : "system", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000028", "ISBN:978-0674639416" ] + "val" : "A material entity consisting of multiple components that are causally integrated." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heterochrony", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "heterochronous homologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000028" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.jbiomedsem.com/content/4/1/43" } ] - }, - "type" : "PROPERTY", - "lbl" : "in heterochronous homology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000029", - "meta" : { - "definition" : { - "val" : "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.", - "xrefs" : [ "http://en.wikipedia.org/wiki/Pedomorphosis", "http://purl.obolibrary.org/obo/HOM_0000029", "ISBN:978-0674639416" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "juvenification", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "pedomorphosis", - "xrefs" : [ ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000029" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "lbl" : "directly regulates", "type" : "PROPERTY", - "lbl" : "in paedomorphorsis relationship with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000026", "meta" : { "definition" : { - "val" : "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.", - "xrefs" : [ "http://dx.doi.org/10.1006/scdb.1999.0338", "http://dx.doi.org/10.1038/nrg2099", "http://purl.obolibrary.org/obo/HOM_0000026" ] + "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." }, - "comments" : [ "The converse of pro-orthologous." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "semi-orthologous to", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000026" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] - }, - "type" : "PROPERTY", - "lbl" : "in semi-orthology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000027", + "id" : "http://purl.obolibrary.org/obo/RO_0002579", + "lbl" : "is indirect form of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Iterative homology that involves structures arranged along the main body axis.", - "xrefs" : [ "http://dx.doi.org/10.1146/annurev.es.20.110189.000411", "http://purl.obolibrary.org/obo/HOM_0000027" ] + "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "homonomy", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "serial homologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000027" + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "in serial homology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009005", + "id" : "http://purl.obolibrary.org/obo/RO_0002580", + "lbl" : "logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002581", + "lbl" : "is a defining property chain axiom", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-8844-9165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bread 'has primary substance added' some 'flour'" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has primary substance added" + "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009004", + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "sardine has consumer some homo sapiens" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-8844-9165" - } ] - }, + "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002583", + "lbl" : "existence starts at end of", "type" : "PROPERTY", - "lbl" : "has consumer" + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009003", + "id" : "http://purl.obolibrary.org/obo/RO_0002584", + "lbl" : "has part structure that is capable of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.", - "xrefs" : [ ] + "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "sardines 'immersed in' some 'oil and mustard'" + "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-8844-9165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "immersed in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000302", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first.", - "xrefs" : [ ] - }, - "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ], - "deprecated" : true - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002585", + "lbl" : "results in closure of", "type" : "PROPERTY", - "lbl" : "obsolete downstream in neural circuit with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000031", "meta" : { - "definition" : { - "val" : "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.", - "xrefs" : [ "http://en.wikipedia.org/wiki/Progenesis", "http://purl.obolibrary.org/obo/HOM_0000031", "ISBN:978-0674639416" ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000031" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." } ] - }, - "type" : "PROPERTY", - "lbl" : "in progenesis relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002602", + "id" : "http://purl.obolibrary.org/obo/RO_0002586", + "lbl" : "results in breakdown of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.", - "xrefs" : [ ] + "val" : "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" } - }, - "type" : "PROPERTY", - "lbl" : "in approximate one to one relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000301", + "id" : "http://purl.obolibrary.org/obo/RO_0002587", + "lbl" : "results in synthesis of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002588", + "lbl" : "results in assembly of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first.", - "xrefs" : [ ] - }, - "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete upstream in neural circuit with" + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000032", + "id" : "http://purl.obolibrary.org/obo/RO_0002589", + "lbl" : "results in catabolism of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paedomorphosis that is produced by a retardation of somatic development.", - "xrefs" : [ "http://en.wikipedia.org/wiki/Neoteny", "http://purl.obolibrary.org/obo/HOM_0000032", "ISBN:978-0674639416" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "juvenilization", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "neotenous to", - "xrefs" : [ ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000032" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - } ] - }, + "val" : "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002590", + "lbl" : "results in disassembly of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002591", + "lbl" : "results in remodeling of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002592", + "lbl" : "results in organization of", "type" : "PROPERTY", - "lbl" : "in neoteny relationship with" + "meta" : { + "definition" : { + "val" : "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002603", + "id" : "http://purl.obolibrary.org/obo/RO_0002593", + "lbl" : "existence ends at start of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" - } ] - }, + "val" : "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002594", + "lbl" : "is relational form of a class", "type" : "PROPERTY", - "lbl" : "is approximately equivalent to" + "meta" : { + "definition" : { + "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000300", + "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "lbl" : "causal relation between material entity and a process", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.", - "xrefs" : [ ] + "val" : "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." }, - "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete in neural circuit with" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002604", + "id" : "http://purl.obolibrary.org/obo/RO_0002596", + "lbl" : "capable of regulating", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).", - "xrefs" : [ ] + "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" + "val" : "pyrethroid -> growth" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, - "type" : "PROPERTY", - "lbl" : "is opposite of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000030", + "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "lbl" : "capable of negatively regulating", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.", - "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000030" ] + "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000030" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, - "type" : "PROPERTY", - "lbl" : "in peramorphosis relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002605", + "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "lbl" : "capable of positively regulating", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "is indistinguishable from" + "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "renin -> arteriolar smooth muscle contraction" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000036", + "id" : "http://purl.obolibrary.org/obo/RO_0002599", + "lbl" : "capable of inhibiting or preventing pathological process", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Historical homology that involves two members of a larger set of homologs.", - "xrefs" : [ "http://dx.doi.org/10.1093/molbev/msp002", "http://purl.obolibrary.org/obo/HOM_0000036" ] + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "many:many homology ", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "many to many homologous to", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "many-to-many homology", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000036" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pazopanib -> pathological angiogenesis" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." } ] - }, - "type" : "PROPERTY", - "lbl" : "in many to many homology relationship with" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002600", + "lbl" : "capable of upregulating or causing pathological process", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.", - "xrefs" : [ ] + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "benzene -> cancer [CHEBI]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "causes disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002601", + "lbl" : "logical macro assertion involving identity", "type" : "PROPERTY", - "lbl" : "capable of upregulating or causing pathological process" + "meta" : { + "definition" : { + "val" : "A shortcut relationship that holds between two entities based on their identity criteria" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000033", + "id" : "http://purl.obolibrary.org/obo/RO_0002602", + "lbl" : "in approximate one to one relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Convergence that results from co-evolution usually involving an evolutionary arms race.", - "xrefs" : [ "http://en.wikipedia.org/wiki/Mimicry", "http://purl.obolibrary.org/obo/HOM_0000033" ] + "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002603", + "lbl" : "is approximately equivalent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mimicrous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000033" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" } ] - }, - "type" : "PROPERTY", - "lbl" : "in mimicry relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000034", + "id" : "http://purl.obolibrary.org/obo/RO_0002604", + "lbl" : "is opposite of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.", - "xrefs" : [ "http://dx.doi.org/10.1038/415741a", "http://purl.obolibrary.org/obo/HOM_0000034", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] + "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "one-to-many orthology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "1:many orthology", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "co-orthology", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "many to 1 orthology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "1 to many orthologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000034" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" } ] - }, - "type" : "PROPERTY", - "lbl" : "in 1 to many orthology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002601", + "id" : "http://purl.obolibrary.org/obo/RO_0002605", + "lbl" : "is indistinguishable from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A shortcut relationship that holds between two entities based on their identity criteria", - "xrefs" : [ ] + "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." } - }, - "type" : "PROPERTY", - "lbl" : "logical macro assertion involving identity" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002606", + "lbl" : "is substance that treats", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.", - "xrefs" : [ ] + "val" : "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "treats" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" } ] - }, - "type" : "PROPERTY", - "lbl" : "is substance that treats" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002607", + "lbl" : "is marker for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. 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"xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000016", "SO:non_functional_homolog_of" ] - }, - "xrefs" : [ { - "val" : "SO:non_functional_homolog_of" - } ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "pseudogene", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "non functional homologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000016" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "val" : "https://github.com/oborel/obo-relations/issues/74" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002619", + "lbl" : "visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002622", + "lbl" : "visits flowers of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002623", + "lbl" : "has flowers visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002624", + "lbl" : "lays eggs in", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002625", + "lbl" : "has eggs laid in by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002626", + "lbl" : "kills", "type" : "PROPERTY", - "lbl" : "in non functional homology relationship with" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://github.com/jhpoelen/eol-globi-data/issues/143" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000019", + "id" : "http://purl.obolibrary.org/obo/RO_0002627", + "lbl" : "is killed by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "lbl" : "directly positively regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Historical homology that involves two members sharing no other homologs in the lineages considered.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000019", "BGEE:curator" ] + "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "1 to 1 homologous to", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "1:1 homology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "one-to-one homology", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000019" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly positively regulates (process to process)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" } ] - 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The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000013" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003303", + "lbl" : "causes condition", "type" : "PROPERTY", - "lbl" : "in syntenic orthology relationship with" + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000014", + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "lbl" : "contributes to condition", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000014", "ISBN:0123195837", "ISBN:978-0471984931" ] + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "lbl" : "contributes to severity of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "percent homology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "segmental homology", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "mixed homology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "partial homologous to", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "fractional homology", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "modular homology", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "partial correspondence", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000014" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to expressivity of condition" } ] - }, - "type" : "PROPERTY", - "lbl" : "in partial homology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000011", + "id" : "http://purl.obolibrary.org/obo/RO_0003306", + "lbl" : "contributes to frequency of condition", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Historical homology that involves genes that diverged after a duplication event.", - "xrefs" : [ "http://dx.doi.org/10.1016/S0168-9525(00)02005-9", "http://dx.doi.org/10.1146/annurev.genet.39.073003.114725", "http://purl.obolibrary.org/obo/HOM_0000011", "http://www.ncbi.nlm.nih.gov/pubmed/5449325" ] + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." }, - "xrefs" : [ { - "val" : "SO:0000854" - }, { - "val" : "SO:0000859" - }, { - "val" : "SO:paralogous_to" - } ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "paralogous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000011" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to penetrance of condition" } ] - }, - "type" : "PROPERTY", - "lbl" : "in paralogy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000012", + "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "lbl" : "ameliorates condition", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paralogy that involves sets of syntenic blocks.", - "xrefs" : [ "http://dx.doi.org/10.1186/1471-213X-7-100", "http://purl.obolibrary.org/obo/HOM_0000012", "DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y" ] + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "duplicon", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "syntenic paralogous to", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "paralogon", - "xrefs" : [ ] - } ], + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000012" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preventative for condition" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003308", + "lbl" : "correlated with condition", "type" : "PROPERTY", - "lbl" : "in syntenic paralogy relationship with" + "meta" : { + "definition" : { + "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000002", + "id" : "http://purl.obolibrary.org/obo/RO_0003309", + "lbl" : "exacerbates condition", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Similarity that results from independent evolution.", - "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000002" ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "analogy", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "homoplasous to", - "xrefs" : [ ] - } ], + "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003310", + "lbl" : "condition ameliorated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003311", + "lbl" : "condition exacerbated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004000", + "lbl" : "condition has genetic basis in", + "type" : "PROPERTY", + "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000002" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:38:20Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "in homoplasy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000003", + "id" : "http://purl.obolibrary.org/obo/RO_0004001", + "lbl" : "has material basis in gain of function germline mutation in", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814484", "http://dx.doi.org/10.1007/s00427-003-0301-4", "http://dx.doi.org/10.1186/1742-9994-2-15", "http://purl.obolibrary.org/obo/HOM_0000003" ] - }, - "comments" : [ "Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues." ], - "xrefs" : [ { - "val" : "ECO:0000075" - } ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "homocracous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:20Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000003" + "val" : "http://www.orpha.net/ORDO/Orphanet_410295" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410296" } ] - }, - "type" : "PROPERTY", - "lbl" : "in homocracy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "id" : "http://purl.obolibrary.org/obo/RO_0004002", + "lbl" : "has material basis in loss of function germline mutation in", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000000", "BGEE:curator" ] - }, - "xrefs" : [ { - "val" : "ECO:0000041" + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "val" : "SO:similar_to" - } ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "resemblance", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "sameness", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "similar to", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "correspondence", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] - } ], + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004003", + "lbl" : "has material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO: Add homeomorphy axiom" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - 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"synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "functional similarity", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000065" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:46:07Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "in functional equivalence relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000062", + "id" : "http://purl.obolibrary.org/obo/RO_0004023", + "lbl" : "causal relationship with disease as subject", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Historical homology that involves functional equivalent genes with retention of the ancestral function.", - "xrefs" : [ "http://dx.doi.org/10.1093/nar/gkl1043", "http://purl.obolibrary.org/obo/HOM_0000062" ] - }, - "comments" : [ "This may include examples of orthology, paralogy and xenology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "equivalogous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000062" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:50:54Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "in equivalogy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000063", + "id" : "http://purl.obolibrary.org/obo/RO_0004024", + "lbl" : "disease causes disruption of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Historical homology that involves orthologous pairs of interacting molecules in different organisms.", - "xrefs" : [ "http://dx.doi.org/10.1101/gr.1774904", "http://dx.doi.org/10.1126/science.287.5450.116", "http://purl.obolibrary.org/obo/HOM_0000063" ] + "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "interologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes disruption of (disease to process)" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000063" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:51:09Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "in interology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000068", + "id" : "http://purl.obolibrary.org/obo/RO_0004025", + "lbl" : "disease causes dysfunction of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000068", "http://www.ncbi.nlm.nih.gov/pubmed/3065587" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "multiple xenology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "duplicate xenology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "paraxenologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes dysfunction of (disease to anatomical entity)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000068" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:58:20Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "in paraxenology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000069", + "id" : "http://purl.obolibrary.org/obo/RO_0004026", + "lbl" : "disease has location", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000069", "http://www.ncbi.nlm.nih.gov/pubmed/3065587" ] + "val" : "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." }, - "comments" : [ "This phenomenon is usually due to gene conversion process." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "plerologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. 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"synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "iterative homologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000066" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:37:31Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "in iterative homology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011022", + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B.", - "xrefs" : [ ] + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "indirectly regulates quantity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000060", + "id" : "http://purl.obolibrary.org/obo/RO_0004029", + "lbl" : "disease has feature", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.", - "xrefs" : [ "http://dx.doi.org/10.1146/annurev.genet.39.073003.114725", "http://purl.obolibrary.org/obo/HOM_0000060", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] + "val" : "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." }, - "comments" : [ "The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "apparent 1:1 orthology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "apparent orthologous to", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "1:1 paralogy", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "pseudoorthology", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000060" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:50:53Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "in apparent orthology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000061", + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "lbl" : "disease arises from alteration in structure", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.", - "xrefs" : [ "http://dx.doi.org/10.1146/annurev.genet.39.073003.114725", "http://purl.obolibrary.org/obo/HOM_0000061" ] + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." }, - "comments" : [ "These genes may come out as paralogs in a single-genome analysis." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "pseudoparalogous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000061" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "in pseudoparalogy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011023", + "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "lbl" : "enables subfunction", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B.", - "xrefs" : [ ] + "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-25T23:20:13Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "indirectly negatively regulates quantity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011021", + "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "lbl" : "acts upstream of or within, positive effect", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B.", - "xrefs" : [ ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:30Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly regulates quantity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0007000", + "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "lbl" : "acts upstream of or within, negative effect", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity.", - "xrefs" : [ ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/506" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-8910-9851" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:51Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has driver" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011024", + "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "lbl" : "acts upstream of, positive effect", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B.", - "xrefs" : [ ] + "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" } ] - }, - "type" : "PROPERTY", - "lbl" : "indirectly positively regulates quantity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004096", - "meta" : { - "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], - "deprecated" : true - }, + "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "lbl" : "acts upstream of, negative effect", "type" : "PROPERTY", - "lbl" : "DEPRECATED inheres in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000048", "meta" : { "definition" : { - "val" : "Orthology that involves two genes that experienced duplications more recent than the species split that created them.", - "xrefs" : [ "http://dx.doi.org/10.1038/415741a", "http://purl.obolibrary.org/obo/HOM_0000048", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] + "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "co-orthology", - "xrefs" : [ ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { - "pred" : "hasRelatedSynonym", - "val" : "trans-homology", - "xrefs" : [ ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "hasExactSynonym", - "val" : "many-to-many orthology", - "xrefs" : [ ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" }, { - "pred" : "hasExactSynonym", - "val" : "trans-orthology", - "xrefs" : [ ] + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004036", + "lbl" : "nominally disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" }, { - "pred" : "hasExactSynonym", - "val" : "many:many orthology", - "xrefs" : [ ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "hasExactSynonym", - "val" : "many to many orthologous to", - "xrefs" : [ ] - } ], + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000048" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "in many to many orthology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000049", + "id" : "http://purl.obolibrary.org/obo/RO_0004048", + "lbl" : "is directional form of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paralogy that involves genes from the same species.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000049", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] + "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "within-species paralogous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000049" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:59:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004049", + "lbl" : "is positive form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:16Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004096", + "lbl" : "DEPRECATED inheres in", "type" : "PROPERTY", - "lbl" : "in within-species paralogy relationship with" + "meta" : { + "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], + "deprecated" : true + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004097", + "lbl" : "DEPRECATED bearer of", + "type" : "PROPERTY", "meta" : { "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "DEPRECATED bearer of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0007001", + "id" : "http://purl.obolibrary.org/obo/RO_0007000", + "lbl" : "has driver", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes.", - "xrefs" : [ ] + "val" : "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", @@ -11251,6746 +9729,7593 @@ "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/oborel/obo-relations/issues/506" } ] - }, - "type" : "PROPERTY", - "lbl" : "has disease driver" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000053", + "id" : "http://purl.obolibrary.org/obo/RO_0007001", + "lbl" : "has disease driver", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.", - "xrefs" : [ "http://dx.doi.org/10.1007/BF00173425", "http://dx.doi.org/10.1016/S0168-9525(00)02005-9", "http://purl.obolibrary.org/obo/HOM_0000053" ] + "val" : "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "synologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000053" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" } ] - }, - "type" : "PROPERTY", - "lbl" : "in synology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000054", + "id" : "http://purl.obolibrary.org/obo/RO_0008501", + "lbl" : "epiphyte of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Orthology that involves functional equivalent genes with retention of the ancestral function.", - "xrefs" : [ "http://dx.doi.org/10.1016/S0168-9525(00)02005-9", "http://purl.obolibrary.org/obo/HOM_0000054" ] + "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." }, - "xrefs" : [ { - "val" : "ECO:0000080" - } ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "isoorthologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000054" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Epiphyte" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008502", + "lbl" : "has epiphyte", "type" : "PROPERTY", - "lbl" : "in isoorthology relationship with" + "meta" : { + "definition" : { + "val" : "inverse of epiphyte of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000051", + "id" : "http://purl.obolibrary.org/obo/RO_0008503", + "lbl" : "kleptoparasite of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paedomorphosis that is produced by delayed growth of immature structures into the adult form.", - "xrefs" : [ "http://en.wikipedia.org/wiki/Pedomorphosis", "http://purl.obolibrary.org/obo/HOM_0000051" ] + "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "post-displacement", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000051" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008504", + "lbl" : "kleptoparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of kleptoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008505", + "lbl" : "creates habitat for", "type" : "PROPERTY", - "lbl" : "in postdisplacement relationship with" + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000052", + "id" : "http://purl.obolibrary.org/obo/RO_0008506", + "lbl" : "ecologically co-occurs with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Peramorphosis that is produced by a delay in the offset of development.", - "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000052", "ISBN:978-0674639416" ] + "val" : "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008507", + "lbl" : "lays eggs on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008508", + "lbl" : "has eggs laid on by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of lays eggs on" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009001", + "lbl" : "has substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "muffin 'has substance added' some 'baking soda'" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000052" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" } ] - }, - "type" : "PROPERTY", - "lbl" : "in hypermorphosis relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000057", + "id" : "http://purl.obolibrary.org/obo/RO_0009002", + "lbl" : "has substance removed", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character).", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814485", "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://dx.doi.org/10.1186/1742-9994-2-15", "http://purl.obolibrary.org/obo/HOM_0000057", "ISBN:0199141118" ] + "val" : "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." }, - "comments" : [ "Used for structures in closely related taxa." ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "re-awakening", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "cryptic homology", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "homoplastic tendency", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "apomorphic tendency", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "latent homologous to", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "homoiology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "underlying synapomorphy", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'egg white' 'has substance removed' some 'egg yolk'" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000057" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" } ] - }, - "type" : "PROPERTY", - "lbl" : "in latent homology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000058", + "id" : "http://purl.obolibrary.org/obo/RO_0009003", + "lbl" : "immersed in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual.", - "xrefs" : [ "http://dx.doi.org/10.1186/1742-9994-2-15", "http://purl.obolibrary.org/obo/HOM_0000058", "DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R" ] + "val" : "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." }, - "comments" : [ "Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes." ], - 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"synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gametologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000046" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" } ] - }, - "type" : "PROPERTY", - "lbl" : "in gametology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000047", + "id" : "http://purl.obolibrary.org/obo/RO_0011021", + "lbl" : "directly regulates quantity of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Historical homology that involves the chromosomes able to pair (synapse) during meiosis.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000047", "ISBN:0195307615" ] + "val" : "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." }, - "xrefs" : [ { - "val" : "MeSH:Chromosome_Pairing" - } ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chromosomal homologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000047" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" } ] - }, - "type" : "PROPERTY", - "lbl" : "in chromosomal homology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000044", + "id" : "http://purl.obolibrary.org/obo/RO_0011022", + "lbl" : "indirectly regulates quantity of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814485", "http://dx.doi.org/10.1038/nature07891", "http://purl.obolibrary.org/obo/HOM_0000044" ] + "val" : "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." }, - "comments" : [ "Used for structures in distantly related taxa." ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "homoiology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "deep genetic homology", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "generative homology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "deep homologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000044" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" } ] - }, - "type" : "PROPERTY", - "lbl" : "in deep homology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000045", + "id" : "http://purl.obolibrary.org/obo/RO_0011023", + "lbl" : "indirectly negatively regulates quantity of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.", - "xrefs" : [ "http://dx.doi.org/10.1073/pnas.0807433105", "http://purl.obolibrary.org/obo/HOM_0000045" ] + "val" : "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "hemiplasous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000045" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011024", + "lbl" : "indirectly positively regulates quantity of", "type" : "PROPERTY", - "lbl" : "in hemiplasy relationship with" + "meta" : { + "definition" : { + "val" : "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012012", + "id" : "http://purl.obolibrary.org/obo/RO_0012000", + "lbl" : "has small molecule regulator", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.", - "xrefs" : [ ] + "val" : "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2022-09-26T06:08:01Z" + "val" : "2020-04-22T20:27:26Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "indirectly regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012010", + "id" : "http://purl.obolibrary.org/obo/RO_0012001", + "lbl" : "has small molecule activator", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.", - "xrefs" : [ ] + "val" : "a relation between a process and a continuant, in which the process is activated by the small molecule continuant" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2022-09-26T06:06:20Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-04-22T20:28:37Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "removes input for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012011", + "id" : "http://purl.obolibrary.org/obo/RO_0012002", + "lbl" : "has small molecule inhibitor", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.", - "xrefs" : [ ] + "val" : "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2022-09-26T06:07:17Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-04-22T20:28:54Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "indirectly causally upstream of" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "id" : "http://purl.obolibrary.org/obo/RO_0012003", + "lbl" : "acts on population of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a core relation that holds between a part and its whole", - "xrefs" : [ ] + "val" : "p acts on population of c iff c' is a collection, has members of type c, and p has participant c" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is part of my body (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this day is part of this year (occurrent parthood)" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-06-08T17:21:33Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "part of" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "id" : "http://purl.obolibrary.org/obo/RO_0012004", + "lbl" : "is small molecule regulator of", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this disease course realizes this disease" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this investigation realizes this investigator role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "realizes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this shattering realizes this fragility" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/iao.owl" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-06-24T13:15:17Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "realizes" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "id" : "http://purl.obolibrary.org/obo/RO_0012005", + "lbl" : "is small molecule activator of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a core relation that holds between a whole and its part", - "xrefs" : [ ] + "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this year has part this day (occurrent parthood)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has part my brain (continuant parthood, two material entities)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-06-24T13:15:26Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has part" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "id" : "http://purl.obolibrary.org/obo/RO_0012006", + "lbl" : "is small molecule inhibitor of", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" + }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "realized_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this disease is realized in this disease course" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this fragility is realized in this shattering" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is realized by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this investigator role is realized in this investigation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "realized in" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-06-24T13:15:35Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "realized in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001900", + "id" : "http://purl.obolibrary.org/obo/RO_0012007", + "lbl" : "results in adhesion of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.", - "xrefs" : [ ] + "val" : "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-08-27T08:13:59Z" } ] - }, - "type" : "PROPERTY" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "id" : "http://purl.obolibrary.org/obo/RO_0012008", + "lbl" : "results in fusion of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "material entity" + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-02-26T07:28:29Z" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013003", + "id" : "http://purl.obolibrary.org/obo/RO_0012009", + "lbl" : "constitutively upstream of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.", - "xrefs" : [ ] + "val" : "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:45:06Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:01:01Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "sends synaptic output to region" + } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", + "id" : "http://purl.obolibrary.org/obo/RO_0012010", + "lbl" : "removes input for", "type" : "PROPERTY", - "lbl" : "has_narrow_synonym" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013002", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.", - "xrefs" : [ ] + "val" : "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:42:23Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:06:20Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "receives synaptic input in region" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013001", + "id" : "http://purl.obolibrary.org/obo/RO_0012011", + "lbl" : "indirectly causally upstream of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.", - "xrefs" : [ ] + "val" : "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "has synaptic input or output in", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "pg" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:26:52Z" + "val" : "2022-09-26T06:07:17Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has synaptic IO in region" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013007", + "id" : "http://purl.obolibrary.org/obo/RO_0012012", + "lbl" : "indirectly regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.", - "xrefs" : [ ] + "val" : "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "has sensory terminal in", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "has sensory dendrite location", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "has sensory terminal location", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-20T12:10:09Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-09-26T06:08:01Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has sensory dendrite in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "id" : "http://purl.obolibrary.org/obo/RO_0013001", + "lbl" : "has synaptic IO in region", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has synaptic input or output in" + } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "http://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-14T00:03:24Z" + "val" : "2020-07-17T09:26:52Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "is negative form of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013006", + "id" : "http://purl.obolibrary.org/obo/RO_0013002", + "lbl" : "receives synaptic input in region", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion).", - "xrefs" : [ ] + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "http://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:57:27Z" + "val" : "2020-07-17T09:42:23Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "sends synaptic output throughout" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013005", + "id" : "http://purl.obolibrary.org/obo/RO_0013003", + "lbl" : "sends synaptic output to region", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion).", - "xrefs" : [ ] + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:55:36Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:45:06Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "receives synaptic input throughout" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0013004", + "lbl" : "has synaptic IO throughout", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion).", - "xrefs" : [ ] + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:52:19Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:52:19Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has synaptic IO throughout" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013009", + "id" : "http://purl.obolibrary.org/obo/RO_0013005", + "lbl" : "receives synaptic input throughout", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to.", - "xrefs" : [ ] + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." }, - "comments" : [ "Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-05-26T08:41:07Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:55:36Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "sends synaptic output to cell" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013008", + "id" : "http://purl.obolibrary.org/obo/RO_0013006", + "lbl" : "sends synaptic output throughout", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it.", - "xrefs" : [ ] + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "http://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-05-26T08:40:18Z" + "val" : "2020-07-17T09:57:27Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "receives synaptic input from neuron" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "id" : "http://purl.obolibrary.org/obo/RO_0013007", + "lbl" : "has sensory dendrite in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.", - "xrefs" : [ ] + "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6996-0040" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-8461-9745" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "has sensory dendrite location" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." + "pred" : "hasExactSynonym", + "val" : "has sensory terminal in" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + "pred" : "hasExactSynonym", + "val" : "has sensory terminal location" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-20T12:10:09Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "realized in response to" + } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", + "id" : "http://purl.obolibrary.org/obo/RO_0013008", + "lbl" : "receives synaptic input from neuron", "type" : "PROPERTY", - "lbl" : "has_obo_format_version" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004047", "meta" : { + "definition" : { + "val" : "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." + }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "http://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:55:19Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" + "val" : "2021-05-26T08:40:18Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally upstream of or within, positive effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "id" : "http://purl.obolibrary.org/obo/RO_0013009", + "lbl" : "sends synaptic output to cell", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." + }, + "comments" : [ "Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "http://orcid.org/0000-0002-1373-1705" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:55:05Z" + "val" : "2021-05-26T08:41:07Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally upstream of or within, negative effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004049", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-14T00:03:16Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0014001", + "lbl" : "disease has infectious agent", "type" : "PROPERTY", - "lbl" : "is positive form of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004048", "meta" : { "definition" : { - "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"", - "xrefs" : [ ] + "val" : "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:59:29Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "http://orcid.org/0000-0001-5208-3432" } ] - }, - "type" : "PROPERTY", - "lbl" : "is directional form of" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000060", - "meta" : { - "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], - "deprecated" : true - }, + "id" : "http://purl.obolibrary.org/obo/RO_0015001", + "lbl" : "has exemplar data", "type" : "PROPERTY", - "lbl" : "obsolete preceded by" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", "meta" : { "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", - "xrefs" : [ ] + "val" : "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-5260-9315" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is not meant to capture the relation between occurrents and data." } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015002", + "lbl" : "exemplar data of", "type" : "PROPERTY", - "lbl" : "occurs in" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-5260-9315" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "id" : "http://purl.obolibrary.org/obo/RO_0015003", + "lbl" : "subcluster of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", - "xrefs" : [ ] + "val" : "A relation between a group and another group it is part of but does not fully constitute." }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7258-9596" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." } ] - }, - "type" : "PROPERTY", - "lbl" : "contains process" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", - "xrefs" : [ ] + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" } ] - }, - "type" : "PROPERTY", - "lbl" : "preceded by" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "id" : "http://purl.obolibrary.org/obo/RO_0015006", + "lbl" : "different in magnitude relative to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" - } ] - }, - "type" : "PROPERTY", - "lbl" : "precedes" + "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002091", - "meta" : { - "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "io" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0015007", + "lbl" : "increased in magnitude relative to", "type" : "PROPERTY", - "lbl" : "starts during" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000019", - "type" : "CLASS", - "lbl" : "quality" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002092", "meta" : { - "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "during" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "d" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - } ] - }, - "type" : "PROPERTY", - "lbl" : "happens during" + "definition" : { + "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "lbl" : "decreased in magnitude relative to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.", - "xrefs" : [ ] + "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:58:44Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "disease arises from alteration in structure" + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002093", - "meta" : { - "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "o" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "overlaps" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0015009", + "lbl" : "similar in magnitude relative to", "type" : "PROPERTY", - "lbl" : "ends during" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "meta" : { "definition" : { - "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.", - "xrefs" : [ ] + "val" : "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } - }, - "type" : "CLASS", - "lbl" : "process" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000016", - "type" : "CLASS", - "lbl" : "disposition" + "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "lbl" : "has relative magnitude", + "type" : "PROPERTY" }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "id" : "http://purl.obolibrary.org/obo/RO_0015011", + "lbl" : "has cross section", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "realizable entity" + "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002090", - "meta" : { - "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends_at_start_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "meets" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/BFO_0000063" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0015012", + "lbl" : "reciprocal of", "type" : "PROPERTY", - "lbl" : "immediately precedes" + "meta" : { + "definition" : { + "val" : "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality." ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004036", + "id" : "http://purl.obolibrary.org/obo/RO_0015015", + "lbl" : "has high plasma membrane amount", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation.", - "xrefs" : [ ] + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" } ] - }, - "type" : "PROPERTY", - "lbl" : "nominally disjoint with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "lbl" : "has low plasma membrane amount", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative", - "xrefs" : [ ] + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:53:22Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" } ] - }, - "type" : "PROPERTY", - "lbl" : "acts upstream of, negative effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "id" : "http://purl.obolibrary.org/obo/RO_0016001", + "lbl" : "has phenotype or disease", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:14Z" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:49:30Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" } ] - }, - "type" : "PROPERTY", - "lbl" : "acts upstream of or within, positive effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "id" : "http://purl.obolibrary.org/obo/RO_0016002", + "lbl" : "has disease", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.", - "xrefs" : [ ] + "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-25T23:20:13Z" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:44Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" } ] - }, - "type" : "PROPERTY", - "lbl" : "enables subfunction" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "id" : "http://purl.obolibrary.org/obo/RO_0016004", + "lbl" : "has exposure medium", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive", - "xrefs" : [ ] + "val" : "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000083" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-12-14T20:41:45Z" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:53:14Z" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7463-6306" } ] - }, - "type" : "PROPERTY", - "lbl" : "acts upstream of, positive effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "id" : "http://purl.obolibrary.org/obo/RO_0017001", + "lbl" : "device utilizes material", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "definition" : { + "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "utilizes" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A diagnostic testing device utilizes a specimen." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-2620-0345" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:49:51Z" + "val" : "2021-11-08T12:00:00Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "acts upstream of or within, negative effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004029", + "id" : "http://purl.obolibrary.org/obo/RO_0018001", + "lbl" : "is myristoyltransferase activity", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.", - "xrefs" : [ ] + "val" : "Helper relation for OWL definition of RO:0018002 myristoylates" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:50:53Z" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has feature" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008508", - "meta" : { - "definition" : { - "val" : "inverse of lays eggs on", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "has eggs laid on by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008507", - "meta" : { - "definition" : { - "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0018002", + "lbl" : "myristoylates", "type" : "PROPERTY", - "lbl" : "lays eggs on" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004028", "meta" : { "definition" : { - "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.", - "xrefs" : [ ] + "val" : "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/terms/conformsTo", + "val" : "http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:45:49Z" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] - }, - "type" : "PROPERTY", - "lbl" : "realized in response to stimulus" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008506", - "meta" : { - "definition" : { - "val" : "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "ecologically co-occurs with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008505", - "meta" : { - "definition" : { - "val" : "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0018003", + "lbl" : "myristoylated by", "type" : "PROPERTY", - "lbl" : "creates habitat for" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0014001", "meta" : { "definition" : { - "val" : "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent.", - "xrefs" : [ ] + "val" : "inverse of myristoylates" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has infectious agent" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "id" : "http://purl.obolibrary.org/obo/RO_0018027", + "lbl" : "is agonist of", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Primitive instance level timing relation between events" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "<=" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P3772" } ] - }, - "type" : "PROPERTY", - "lbl" : "before or simultaneous with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "id" : "http://purl.obolibrary.org/obo/RO_0018028", + "lbl" : "is inverse agonist of", + "type" : "PROPERTY", "meta" : { - "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P9275" } ] - }, - "type" : "PROPERTY", - "lbl" : "simultaneous with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002083", - "meta" : { - "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0018029", + "lbl" : "is antagonist of", "type" : "PROPERTY", - "lbl" : "before" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000004", - "meta" : { - "definition" : { - "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "independent continuant" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000006", - "type" : "CLASS", - "lbl" : "spatial region" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008504", "meta" : { "definition" : { - "val" : "inverse of kleptoparasite of", - "xrefs" : [ ] + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "kleptoparasitized by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004025", - "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease causes dysfunction of (disease to anatomical entity)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:58:20Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P3773" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease causes dysfunction of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002088", - "meta" : { - "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0019000", + "lbl" : "regulates characteristic", "type" : "PROPERTY", - "lbl" : "during which starts" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008503", "meta" : { "definition" : { - "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material", - "xrefs" : [ ] + "val" : "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] - }, - "type" : "PROPERTY", - "lbl" : "kleptoparasite of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004024", + "id" : "http://purl.obolibrary.org/obo/RO_0019001", + "lbl" : "positively regulates characteristic", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process.", - "xrefs" : [ ] + "val" : "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:51:09Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease causes disruption of (disease to process)" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease causes disruption of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002089", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0019002", + "lbl" : "negatively regulates characteristic", "type" : "PROPERTY", - "lbl" : "starts before" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008502", "meta" : { "definition" : { - "val" : "inverse of epiphyte of", - "xrefs" : [ ] + "val" : "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "has epiphyte" + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004027", + "id" : "http://purl.obolibrary.org/obo/RO_0019501", + "lbl" : "confers susceptibility to condition", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity", - "xrefs" : [ ] + "val" : "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:37:31Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "http://orcid.org/0000-0002-4142-7153" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has inflammation site" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004026", + "id" : "http://purl.obolibrary.org/obo/RO_0040035", + "lbl" : "disease relationship", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.", - "xrefs" : [ ] + "val" : "This relation groups relations between diseases and any other kind of entity." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T04:06:02Z" + "val" : "2018-09-26T00:00:32Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has location" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008501", + "id" : "http://purl.obolibrary.org/obo/RO_0040036", + "lbl" : "results in changes to anatomical or cellular structure", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant.", - "xrefs" : [ ] + "val" : "p has anatomical participant c iff p has participant c, and c is an anatomical entity" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Epiphyte" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T01:08:58Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "epiphyte of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004021", + "id" : "http://purl.obolibrary.org/obo/RO_0040042", + "lbl" : "is homeomorphic for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.", - "xrefs" : [ ] + "val" : "R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C." }, + "comments" : [ "R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:37:52Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease has basis in disruption of (disease to process)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part-of is homeomorphic for independent continuants." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-10-21T19:46:34Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/164" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has basis in disruption of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002084", - "meta" : { - "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "lbl" : "in similarity relationship with", "type" : "PROPERTY", - "lbl" : "during which ends" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002085", "meta" : { - "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "definition" : { + "val" : "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000000", "BGEE:curator" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "sameness" + }, { + "pred" : "hasExactSynonym", + "val" : "similar to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "correspondence", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "resemblance" + } ], + "xrefs" : [ { + "val" : "ECO:0000041" + }, { + "val" : "SO:similar_to" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add homeomorphy axiom" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "di" + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000000" } ] - }, - "type" : "PROPERTY", - "lbl" : "encompasses" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004020", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000001", + "lbl" : "in homology relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.", - "xrefs" : [ ] + "val" : "Similarity that results from common evolutionary origin.", + "xrefs" : [ "http://dx.doi.org/10.1002/bies.950180611", "http://dx.doi.org/10.1002/jmor.1051730307", "http://dx.doi.org/10.1007/BF02814480", "http://purl.obolibrary.org/obo/HOM_0000001" ] }, + "comments" : [ "This broad definition encompasses all the working definitions proposed so far in the literature." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homologous to" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease has basis in dysfunction of (disease to anatomical structure)" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:29:32Z" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000001" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has basis in dysfunction of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004023", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000002", + "lbl" : "in homoplasy relationship with", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Similarity that results from independent evolution.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000002" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homoplasous to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "analogy" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:50:54Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000002" } ] - }, - "type" : "PROPERTY", - "lbl" : "causal relationship with disease as subject" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002086", - "meta" : { - "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000003", + "lbl" : "in homocracy relationship with", "type" : "PROPERTY", - "lbl" : "ends after" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002087", "meta" : { - "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "definition" : { + "val" : "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814484", "http://dx.doi.org/10.1007/s00427-003-0301-4", "http://dx.doi.org/10.1186/1742-9994-2-15", "http://purl.obolibrary.org/obo/HOM_0000003" ] + }, + "comments" : [ "Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homocracous to" + } ], + "xrefs" : [ { + "val" : "ECO:0000075" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts_at_end_of" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000003" } ] - }, - "type" : "PROPERTY", - "lbl" : "immediately preceded by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004022", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000004", + "lbl" : "in convergence relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.", - "xrefs" : [ ] + "val" : "Homoplasy that involves different underlying mechanisms or structures.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000004" ] }, + "comments" : [ "Convergence usually implies a notion of adaptation." ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "analogy" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:46:07Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has basis in feature" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004018", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:20:29Z" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000004" } ] - }, - "type" : "PROPERTY", - "lbl" : "is basis for realizable" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004017", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000005", + "lbl" : "in parallelism relationship with", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Homoplasy that involves homologous underlying mechanisms or structures.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000005" ] + }, + "comments" : [ "Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "parallel evolution" + } ], "basicPropertyValues" : [ { - 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"http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000062" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/RO_0002082" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002333" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000063" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/BFO_0000050" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002509", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002507", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002428", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002331", "http://purl.obolibrary.org/obo/RO_0002211" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002205", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002511", "http://purl.obolibrary.org/obo/RO_0002513" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0015001", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0015001", "http://purl.obolibrary.org/obo/RO_0015003" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002204", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002512", "http://purl.obolibrary.org/obo/RO_0002510" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002090", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002230", "http://purl.obolibrary.org/obo/RO_0002224" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002526", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002524", "http://purl.obolibrary.org/obo/RO_0002525" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013007", "http://purl.obolibrary.org/obo/BFO_0000050" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002583", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002403", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002402" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002593", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/BFO_0000066" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002400", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002224", "http://purl.obolibrary.org/obo/RO_0002400" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002480", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002482", "http://purl.obolibrary.org/obo/RO_0002400" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002598", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002213" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002554", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002445", "http://purl.obolibrary.org/obo/RO_0002445" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004024", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002593", "http://purl.obolibrary.org/obo/BFO_0000050" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002110", "http://purl.obolibrary.org/obo/BFO_0000050" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002447", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002481", "http://purl.obolibrary.org/obo/RO_0002400" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002011", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002211", "http://purl.obolibrary.org/obo/RO_0002313" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000062" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000055", "http://purl.obolibrary.org/obo/RO_0000052" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013002", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0002162" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013003", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013003", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002211", "http://purl.obolibrary.org/obo/RO_0019000" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013007", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002211", "http://purl.obolibrary.org/obo/RO_0002025" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0015001", "http://purl.obolibrary.org/obo/RO_0015003" ] } ] } ] } \ No newline at end of file diff --git a/ro-base.obo b/ro-base.obo index ac913ed9..834cc834 100644 --- a/ro-base.obo +++ b/ro-base.obo @@ -6,37 +6,29 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 310 Logical Axioms: 68] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 3 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] ontology: ro/ro-base property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string +property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) +property_value: owl:versionInfo "2023-02-19" xsd:string [Term] id: BFO:0000002 name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] disjoint_from: BFO:0000003 ! occurrent -relationship: BFO:0000050 BFO:0000002 ! part of continuant -relationship: RO:0002214 BFO:0000002 ! has prototype continuant -relationship: RO:HOM0000000 BFO:0000002 ! continuant +relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant +relationship: RO:0002214 BFO:0000002 {all_only="true"} ! has prototype continuant +relationship: RO:HOM0000000 BFO:0000002 {all_only="true"} ! continuant [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: BFO:0000050 BFO:0000003 ! part of occurrent -relationship: RO:HOM0000000 BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent +relationship: RO:HOM0000000 BFO:0000003 {all_only="true"} ! occurrent [Term] id: BFO:0000004 @@ -45,7 +37,7 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000004 ! part of independent continuant +relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant [Term] id: BFO:0000006 @@ -57,7 +49,7 @@ id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] is_a: BFO:0000003 ! occurrent -relationship: RO:0002214 BFO:0000015 ! has prototype process +relationship: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process [Term] id: BFO:0000016 @@ -71,13 +63,13 @@ name: realizable entity def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality -relationship: BFO:0000050 BFO:0000017 ! part of realizable entity +relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant -relationship: BFO:0000050 BFO:0000019 ! part of quality +relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 @@ -85,7 +77,7 @@ name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant [Term] id: BFO:0000023 @@ -98,7 +90,7 @@ id: BFO:0000031 name: generically dependent continuant def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] is_a: BFO:0000002 ! continuant -relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant +relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant [Term] id: BFO:0000034 @@ -139,7 +131,7 @@ property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-660 property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/pull/173 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/173" xsd:anyURI created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:55:39Z @@ -173,7 +165,7 @@ def: "A material entity consisting of multiple components that are causally inte is_a: BFO:0000040 ! material entity property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string +property_value: IAO:0000119 "http://www.jbiomedsem.com/content/4/1/43" xsd:string [Typedef] id: BFO:0000050 @@ -201,7 +193,7 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf -property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string is_transitive: true is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part @@ -266,7 +258,7 @@ id: BFO:0000062 name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string @@ -365,7 +357,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -613,7 +605,7 @@ id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string @@ -686,7 +678,7 @@ is_a: RO:0001018 ! contained in [Typedef] id: RO:0002005 name: innervated_by -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI +property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: CARO:0000003 range: CARO:0001001 @@ -1317,7 +1309,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_symmetric: true @@ -1423,7 +1415,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -1433,8 +1425,8 @@ name: connected to def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -1444,8 +1436,8 @@ def: "c connects a if and only if there exist some b such that a and b are simil property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 ! independent continuant is_a: RO:0002323 ! mereotopologically related to @@ -1775,7 +1767,7 @@ id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra @@ -1955,28 +1947,28 @@ is_a: RO:0000057 ! has participant id: RO:0002240 name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002241 name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: RO:0002309 ! has exposure stimulus [Typedef] id: RO:0002242 name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002243 name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: RO:0002244 ! related via exposure to [Typedef] @@ -2071,7 +2063,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -2217,7 +2209,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2231,7 +2223,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -2247,7 +2239,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2262,7 +2254,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2382,7 +2374,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2734,7 +2726,7 @@ is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps @@ -2754,7 +2746,7 @@ id: RO:0002372 name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: RO:0002371 ! attached to @@ -2765,7 +2757,7 @@ id: RO:0002373 name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: RO:0002371 ! attached to @@ -2793,7 +2785,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002323 ! mereotopologically related to @@ -2810,11 +2802,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with @@ -2829,7 +2821,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with @@ -2861,7 +2853,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 holds_over_chain: RO:0002377 RO:0002381 is_a: BFO:0000050 ! part of @@ -3113,7 +3105,7 @@ name: differs in comment: This is an exploratory relation property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions xsd:anyURI +property_value: seeAlso "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" xsd:anyURI [Typedef] id: RO:0002425 @@ -3204,12 +3196,12 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true @@ -3217,7 +3209,7 @@ is_symmetric: true [Typedef] id: RO:0002435 name: genetically interacts with -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 @@ -3228,7 +3220,7 @@ is_a: RO:0002434 ! interacts with id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3244,7 +3236,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true @@ -3272,8 +3264,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002458 ! preyed upon by @@ -3283,7 +3275,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -3294,7 +3286,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -3303,7 +3295,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -3312,7 +3304,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -3324,7 +3316,7 @@ synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002454 ! has host inverse_of: RO:0002445 ! parasitized by @@ -3337,7 +3329,7 @@ synonym: "directly parasitized by" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002453 ! host of @@ -3427,7 +3419,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -3438,7 +3430,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: RO:0002442 ! mutualistically interacts with inverse_of: RO:0002456 ! pollinated by @@ -3449,7 +3441,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: RO:0002442 ! mutualistically interacts with [Typedef] @@ -3470,8 +3462,8 @@ subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: RO:0002438 ! trophically interacts with [Typedef] @@ -3864,7 +3856,7 @@ id: RO:0002510 name: transcribed from def: "x is transcribed from y if and only if x is synthesized from template y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002511 ! transcribed to @@ -3874,7 +3866,7 @@ name: transcribed to def: "inverse of transcribed from" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to [Typedef] @@ -3882,7 +3874,7 @@ id: RO:0002512 name: ribosomal translation of def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002513 ! ribosomally translates to @@ -3891,7 +3883,7 @@ id: RO:0002513 name: ribosomally translates to def: "inverse of ribosomal translation of" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to [Typedef] @@ -3900,7 +3892,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 ! sequentially ordered entity @@ -3915,7 +3907,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002527 ! does not overlap sequence of [Typedef] @@ -3926,7 +3918,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002524 ! has subsequence inverse_of: RO:0002517 ! is start sequence of @@ -3939,7 +3931,7 @@ subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002525 ! is subsequence of @@ -3951,7 +3943,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002524 ! has subsequence inverse_of: RO:0002519 ! is end sequence of @@ -3964,7 +3956,7 @@ subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002525 ! is subsequence of @@ -3975,7 +3967,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002524 ! has subsequence [Typedef] @@ -4016,7 +4008,7 @@ def: "x has subsequence y iff all of the sequence parts of y are sequence parts property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002522 ! bounds sequence of @@ -4128,8 +4120,8 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string holds_over_chain: RO:0002444 RO:0002444 is_a: RO:0002454 ! has host inverse_of: RO:0002554 ! hyperparasitized by @@ -4152,8 +4144,8 @@ id: RO:0002555 name: allelopath of subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -4197,7 +4189,7 @@ id: RO:0002563 name: interaction relation helper property property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] @@ -4244,7 +4236,7 @@ id: RO:0002568 name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: RO:0002567 ! biomechanically related to [Typedef] @@ -4264,7 +4256,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -4276,7 +4268,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -4521,7 +4513,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping [Typedef] id: RO:0002618 name: visits -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002619 ! visited by @@ -4557,7 +4549,7 @@ is_a: RO:0002619 ! visited by [Typedef] id: RO:0002626 name: kills -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002627 ! is killed by @@ -4596,7 +4588,7 @@ is_a: RO:0002578 ! directly regulates id: RO:0002632 name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002444 ! parasite of inverse_of: RO:0002633 ! has ectoparasite @@ -4612,7 +4604,7 @@ id: RO:0002634 name: endoparasite of synonym: "lives inside of" RELATED [] property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002444 ! parasite of inverse_of: RO:0002635 ! has endoparasite @@ -4639,7 +4631,7 @@ is_a: RO:0002445 ! parasitized by id: RO:0002638 name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002639 ! has intercellular endoparasite @@ -4654,7 +4646,7 @@ is_a: RO:0002635 ! has endoparasite id: RO:0002640 name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002641 ! has intracellular endoparasite @@ -5187,7 +5179,7 @@ is_a: RO:0007000 ! has driver id: RO:0008501 name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: RO:0002440 ! symbiotically interacts with inverse_of: RO:0008502 ! has epiphyte @@ -5202,7 +5194,7 @@ is_a: RO:0002440 ! symbiotically interacts with id: RO:0008503 name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: RO:0002444 ! parasite of inverse_of: RO:0008504 ! kleptoparasitized by @@ -5305,7 +5297,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 ! realizable entity range: BFO:0000015 ! process holds_over_chain: BFO:0000054 RO:0002404 @@ -5790,25 +5782,25 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0016001 name: has phenotype or disease property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease [Typedef] id: RO:0016004 name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: RO:0002244 ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 diff --git a/ro-base.owl b/ro-base.owl index 13478aaf..d5a4526f 100644 --- a/ro-base.owl +++ b/ro-base.owl @@ -21,16 +21,9 @@ The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology + - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/bfo-axioms.owl>) VersionIRI(<null>))) [Axioms: 18 Logical Axioms: 7] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/bfo-classes-minimal.owl>) VersionIRI(<null>))) [Axioms: 49 Logical Axioms: 12] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/chemical.owl>) VersionIRI(<null>))) [Axioms: 9 Logical Axioms: 3] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/core.owl>) VersionIRI(<null>))) [Axioms: 310 Logical Axioms: 68] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/el-constraints.owl>) VersionIRI(<null>))) [Axioms: 6 Logical Axioms: 2] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/generated-axioms.owl>) VersionIRI(<null>))) [Axioms: 18 Logical Axioms: 9] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/omo_import.owl>) VersionIRI(<null>))) [Axioms: 3 Logical Axioms: 0] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/rohom.owl>) VersionIRI(<null>))) [Axioms: 731 Logical Axioms: 148] - Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ro/temporal-intervals.owl>) VersionIRI(<null>))) [Axioms: 146 Logical Axioms: 45] + 2023-02-19 https://github.com/oborel/obo-relations/ @@ -68,7 +61,7 @@ - definition + definition @@ -144,10 +137,7 @@ - - Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. - defined by construct - + @@ -155,6 +145,7 @@ An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + temporal interpretation @@ -170,7 +161,7 @@ Class: ?X DisjointWith: RO_0002162 some ?Y - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> @@ -193,7 +184,7 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . } - never in taxon + never in taxon @@ -208,7 +199,7 @@ WHERE { shares no parts with Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) - PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { @@ -277,7 +268,7 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> @@ -869,7 +860,7 @@ Where we have an annotation assertion - pg + pg 2020-09-22T11:05:29Z valid_for_go_annotation_extension @@ -881,7 +872,7 @@ Where we have an annotation assertion - pg + pg 2020-09-22T11:05:18Z valid_for_go_gp2term @@ -893,7 +884,7 @@ Where we have an annotation assertion - pg + pg 2020-09-22T11:04:12Z valid_for_go_ontology @@ -905,7 +896,7 @@ Where we have an annotation assertion - pg + pg 2020-09-22T11:05:45Z valid_for_gocam @@ -960,6 +951,18 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -1017,7 +1020,7 @@ Where we have an annotation assertion - subset_property + subset_property @@ -1043,7 +1046,7 @@ Where we have an annotation assertion - has_broad_synonym + has_broad_synonym @@ -1051,7 +1054,7 @@ Where we have an annotation assertion - database_cross_reference + database_cross_reference @@ -1059,7 +1062,7 @@ Where we have an annotation assertion - has_exact_synonym + has_exact_synonym @@ -1067,7 +1070,7 @@ Where we have an annotation assertion - has_narrow_synonym + has_narrow_synonym @@ -1075,7 +1078,7 @@ Where we have an annotation assertion - has_obo_format_version + has_obo_format_version @@ -1083,7 +1086,7 @@ Where we have an annotation assertion - has_related_synonym + has_related_synonym @@ -1097,7 +1100,7 @@ Where we have an annotation assertion - in_subset + in_subset @@ -1892,7 +1895,7 @@ range: spatial region or site (immaterial continuant) A relation that holds between two neurons that are electrically coupled via gap junctions. - electrically_synapsed_to + electrically_synapsed_to @@ -1903,7 +1906,7 @@ range: spatial region or site (immaterial continuant) - The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). tracheates @@ -1994,7 +1997,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label @@ -2069,7 +2072,7 @@ AND t has_input y A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + dos 2017-05-24T09:30:46Z has regulatory component activity @@ -2082,7 +2085,7 @@ AND t has_input y A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity @@ -2096,7 +2099,7 @@ AND t has_input y A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity @@ -2109,7 +2112,7 @@ AND t has_input y - dos + dos 2017-05-24T09:36:08Z A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. has necessary component activity @@ -2121,7 +2124,7 @@ AND t has_input y - dos + dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity @@ -2136,7 +2139,7 @@ AND t has_input y w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + dos 2017-05-24T09:49:21Z has component process @@ -2148,7 +2151,7 @@ AND t has_input y A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - dos + dos 2017-07-19T17:30:36Z has ligand @@ -2160,7 +2163,7 @@ AND t has_input y Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - dos + dos 2017-07-20T17:11:08Z transports @@ -2172,7 +2175,7 @@ AND t has_input y A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - dos + dos 2017-07-20T17:19:37Z occurs across @@ -2184,7 +2187,7 @@ AND t has_input y - dos + dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by @@ -2193,7 +2196,7 @@ AND t has_input y Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + GOC:dos @@ -2204,7 +2207,7 @@ AND t has_input y Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + dos 2017-09-17T13:52:38Z directly negatively regulated by @@ -2212,7 +2215,7 @@ AND t has_input y Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + GOC:dos @@ -2223,7 +2226,7 @@ AND t has_input y Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + dos 2017-09-17T13:52:47Z directly positively regulated by @@ -2231,7 +2234,7 @@ AND t has_input y Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + GOC:dos @@ -2242,7 +2245,7 @@ AND t has_input y A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity @@ -2251,7 +2254,7 @@ AND t has_input y A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + GOC:dos @@ -2270,7 +2273,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - dos + dos 2017-12-07T12:58:06Z in register with @@ -2285,7 +2288,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - GOC:dos + GOC:dos @@ -2521,7 +2524,7 @@ Examples include: the relationship between two channels collected simultaneously fasciculates with - (forall (?x ?y) + (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) @@ -2956,7 +2959,7 @@ N1 SubclassOf ( The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. has fasciculating component - (forall (?x ?y) + (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) @@ -3015,7 +3018,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - X continuous_with Y if and only if X and Y share a fiat boundary. + X continuous_with Y if and only if X and Y share a fiat boundary. connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -3033,8 +3036,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) + proper overlaps + (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and @@ -3055,10 +3058,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. - ancestral_stucture_of - evolutionarily_descended_from - derived by descent from + d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + ancestral_stucture_of + evolutionarily_descended_from + derived by descent from @@ -3071,7 +3074,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of derived by descent from - has derived by descendant + has derived by descendant @@ -3087,10 +3090,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. Consider obsoleting and merging with child relation, 'in homology relationship with' - VBO calls this homologous_to - shares ancestor with + VBO calls this homologous_to + shares ancestor with @@ -3102,7 +3105,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - serially homologous to + serially homologous to @@ -3120,7 +3123,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - only in taxon + only in taxon @@ -3174,8 +3177,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Connects a biological entity to its taxon of origin. - in taxon + Connects a biological entity to its taxon of origin. + in taxon @@ -3194,7 +3197,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - spatially disjoint from + spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -3716,8 +3719,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. agent in - Obsoleted as the inverse property was obsoleted. - obsolete actively participates in + Obsoleted as the inverse property was obsoleted. + obsolete actively participates in true @@ -3730,7 +3733,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has agent - obsolete has active participant + obsolete has active participant true @@ -5087,7 +5090,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. exports @@ -5574,7 +5577,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect input + obsolete has indirect input true @@ -5588,7 +5591,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. directly produces - obsolete has direct output + obsolete has direct output true @@ -5605,7 +5608,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output + obsolete has indirect output true @@ -5642,7 +5645,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This term was obsoleted because it has the same meaning as 'directly positively regulates'. + This term was obsoleted because it has the same meaning as 'directly positively regulates'. obsolete directly activates true @@ -5684,7 +5687,7 @@ https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/ - This term was obsoleted because it has the same meaning as 'directly negatively regulates'. + This term was obsoleted because it has the same meaning as 'directly negatively regulates'. obsolete directly inhibits true @@ -5991,8 +5994,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos + GOC:cjm + GOC:dos @@ -6015,8 +6018,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Considering relabeling as 'pairwise interacts with' Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with @@ -6801,9 +6804,9 @@ the a supports either the existence of b, or the truth value of b. - x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - exists during + exists during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -8074,7 +8077,7 @@ the a supports either the existence of b, or the truth value of b. A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - obsolete related via dependence to + obsolete related via dependence to true @@ -8373,10 +8376,10 @@ the a supports either the existence of b, or the truth value of b. - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces @@ -8676,8 +8679,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -8700,8 +8703,8 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:cjm - GOC:dph + GOC:cjm + GOC:dph GOC:kva GOC:pt PMID:27812932 @@ -9636,8 +9639,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg 2020-04-22T20:27:26Z has small molecule regulator @@ -9649,8 +9652,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg 2020-04-22T20:28:37Z has small molecule activator @@ -9662,8 +9665,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - pg + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg 2020-04-22T20:28:54Z has small molecule inhibitor @@ -9674,8 +9677,8 @@ For example, protein A (transcription factor) indirectly increases by expression - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - pg + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg 2020-06-08T17:21:33Z @@ -9689,8 +9692,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg 2020-06-24T13:15:17Z is small molecule regulator of @@ -9702,8 +9705,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg 2020-06-24T13:15:26Z is small molecule activator of @@ -9715,8 +9718,8 @@ For example, protein A (transcription factor) indirectly increases by expression - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - pg + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg 2020-06-24T13:15:35Z is small molecule inhibitor of @@ -9727,8 +9730,8 @@ For example, protein A (transcription factor) indirectly increases by expression - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - pg + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg 2020-08-27T08:13:59Z results in adhesion of @@ -9739,7 +9742,7 @@ For example, protein A (transcription factor) indirectly increases by expression - pg + pg 2021-02-26T07:28:29Z @@ -9754,7 +9757,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - pg + pg 2022-09-26T06:01:01Z @@ -9768,7 +9771,7 @@ For example, protein A (transcription factor) indirectly increases by expression p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - pg + pg 2022-09-26T06:06:20Z @@ -9782,7 +9785,7 @@ For example, protein A (transcription factor) indirectly increases by expression p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + pg 2022-09-26T06:07:17Z indirectly causally upstream of @@ -9795,7 +9798,7 @@ For example, protein A (transcription factor) indirectly increases by expression p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + pg 2022-09-26T06:08:01Z indirectly regulates @@ -10032,7 +10035,7 @@ For example, protein A (transcription factor) indirectly increases by expression q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased in magnitude relative to @@ -10051,7 +10054,7 @@ For example, protein A (transcription factor) indirectly increases by expression q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased in magnitude relative to @@ -10090,7 +10093,7 @@ For example, protein A (transcription factor) indirectly increases by expression s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. - Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. + Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has cross section @@ -10106,7 +10109,7 @@ For example, protein A (transcription factor) indirectly increases by expression q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. - There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal of @@ -10384,32 +10387,32 @@ For example, protein A (transcription factor) indirectly increases by expression - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. TODO: Add homeomorphy axiom - ECO:0000041 - SO:similar_to - sameness - similar to - correspondence - resemblance - in similarity relationship with + ECO:0000041 + SO:similar_to + sameness + similar to + correspondence + resemblance + in similarity relationship with - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - BGEE:curator + BGEE:curator - correspondence + correspondence @@ -10422,18 +10425,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Similarity that results from common evolutionary origin. + Similarity that results from common evolutionary origin. - homologous to - This broad definition encompasses all the working definitions proposed so far in the literature. - in homology relationship with + homologous to + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with - Similarity that results from common evolutionary origin. + Similarity that results from common evolutionary origin. @@ -10447,18 +10450,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Similarity that results from independent evolution. + Similarity that results from independent evolution. - homoplasous to - analogy - in homoplasy relationship with + homoplasous to + analogy + in homoplasy relationship with - Similarity that results from independent evolution. + Similarity that results from independent evolution. @@ -10471,19 +10474,19 @@ For example, protein A (transcription factor) indirectly increases by expression - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - ECO:0000075 - homocracous to - Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. - in homocracy relationship with + ECO:0000075 + homocracous to + Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + in homocracy relationship with - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. @@ -10497,18 +10500,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Homoplasy that involves different underlying mechanisms or structures. + Homoplasy that involves different underlying mechanisms or structures. - analogy - Convergence usually implies a notion of adaptation. - in convergence relationship with + analogy + Convergence usually implies a notion of adaptation. + in convergence relationship with - Homoplasy that involves different underlying mechanisms or structures. + Homoplasy that involves different underlying mechanisms or structures. @@ -10520,18 +10523,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Homoplasy that involves homologous underlying mechanisms or structures. + Homoplasy that involves homologous underlying mechanisms or structures. - parallel evolution - Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. - in parallelism relationship with + parallel evolution + Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + in parallelism relationship with - Homoplasy that involves homologous underlying mechanisms or structures. + Homoplasy that involves homologous underlying mechanisms or structures. @@ -10543,24 +10546,24 @@ For example, protein A (transcription factor) indirectly increases by expression - Homology that is defined by similarity with regard to selected structural parameters. + Homology that is defined by similarity with regard to selected structural parameters. - ECO:0000071 - MI:2163 - structural homologous to - idealistic homology - in structural homology relationship with + ECO:0000071 + MI:2163 + structural homologous to + idealistic homology + in structural homology relationship with - Homology that is defined by similarity with regard to selected structural parameters. + Homology that is defined by similarity with regard to selected structural parameters. - ISBN:0123195837 + ISBN:0123195837 @@ -10570,32 +10573,32 @@ For example, protein A (transcription factor) indirectly increases by expression - Homology that is defined by common descent. + Homology that is defined by common descent. - homology - ECO:0000080 - RO_proposed_relation:homologous_to - SO:0000330 - SO:0000853 - SO:0000857 - SO:homologous_to - TAO:homologous_to - cladistic homology - historical homologous to - phylogenetic homology - taxic homology - true homology - in historical homology relationship with + homology + ECO:0000080 + RO_proposed_relation:homologous_to + SO:0000330 + SO:0000853 + SO:0000857 + SO:homologous_to + TAO:homologous_to + cladistic homology + historical homologous to + phylogenetic homology + taxic homology + true homology + in historical homology relationship with - Homology that is defined by common descent. + Homology that is defined by common descent. - ISBN:0123195837 + ISBN:0123195837 @@ -10605,20 +10608,20 @@ For example, protein A (transcription factor) indirectly increases by expression - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - ECO:0000067 - biological homologous to - transformational homology - Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. - in biological homology relationship with + ECO:0000067 + biological homologous to + transformational homology + Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + in biological homology relationship with - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. @@ -10631,19 +10634,19 @@ For example, protein A (transcription factor) indirectly increases by expression - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - atavism - rudiment - reversion - in reversal relationship with + atavism + rudiment + reversion + in reversal relationship with - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. @@ -10655,23 +10658,23 @@ For example, protein A (transcription factor) indirectly increases by expression - Structural homology that is detected by similarity in content and organization between chromosomes. + Structural homology that is detected by similarity in content and organization between chromosomes. - MeSH:Synteny - SO:0000860 - SO:0005858 - syntenic homologous to - synteny - in syntenic homology relationship with + MeSH:Synteny + SO:0000860 + SO:0005858 + syntenic homologous to + synteny + in syntenic homology relationship with - Structural homology that is detected by similarity in content and organization between chromosomes. + Structural homology that is detected by similarity in content and organization between chromosomes. - MeSH:Synteny + MeSH:Synteny @@ -10682,20 +10685,20 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that involves genes that diverged after a duplication event. + Historical homology that involves genes that diverged after a duplication event. - SO:0000854 - SO:0000859 - SO:paralogous_to - paralogous to - in paralogy relationship with + SO:0000854 + SO:0000859 + SO:paralogous_to + paralogous to + in paralogy relationship with - Historical homology that involves genes that diverged after a duplication event. + Historical homology that involves genes that diverged after a duplication event. @@ -10710,22 +10713,22 @@ For example, protein A (transcription factor) indirectly increases by expression - Paralogy that involves sets of syntenic blocks. + Paralogy that involves sets of syntenic blocks. - syntenic paralogous to - duplicon - paralogon - in syntenic paralogy relationship with + syntenic paralogous to + duplicon + paralogon + in syntenic paralogy relationship with - Paralogy that involves sets of syntenic blocks. + Paralogy that involves sets of syntenic blocks. - DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y + DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y @@ -10735,17 +10738,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Syntenic homology that involves chromosomes of different species. + Syntenic homology that involves chromosomes of different species. - syntenic orthologous to - in syntenic orthology relationship with + syntenic orthologous to + in syntenic orthology relationship with - Syntenic homology that involves chromosomes of different species. + Syntenic homology that involves chromosomes of different species. @@ -10757,26 +10760,26 @@ For example, protein A (transcription factor) indirectly increases by expression - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - fractional homology - partial homologous to - segmental homology - mixed homology - modular homology - partial correspondence - percent homology - in partial homology relationship with + fractional homology + partial homologous to + segmental homology + mixed homology + modular homology + partial correspondence + percent homology + in partial homology relationship with - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - ISBN:0123195837 - ISBN:978-0471984931 + ISBN:0123195837 + ISBN:978-0471984931 @@ -10786,18 +10789,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - MeSH:Structural_Homology,_Protein - protein structural homologous to - in protein structural homology relationship with + MeSH:Structural_Homology,_Protein + protein structural homologous to + in protein structural homology relationship with - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. @@ -10810,21 +10813,21 @@ For example, protein A (transcription factor) indirectly increases by expression - Structural homology that involves a pseudogenic feature and its functional ancestor. + Structural homology that involves a pseudogenic feature and its functional ancestor. - pseudogene - SO:non_functional_homolog_of - non functional homologous to - in non functional homology relationship with + pseudogene + SO:non_functional_homolog_of + non functional homologous to + in non functional homology relationship with - Structural homology that involves a pseudogenic feature and its functional ancestor. + Structural homology that involves a pseudogenic feature and its functional ancestor. - SO:non_functional_homolog_of + SO:non_functional_homolog_of @@ -10834,22 +10837,22 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that involves genes that diverged after a speciation event. + Historical homology that involves genes that diverged after a speciation event. - ECO:00000060 - SO:0000855 - SO:0000858 - SO:orthologous_to - orthologous to - The term is sometimes also used for anatomical structures. - in orthology relationship with + ECO:00000060 + SO:0000855 + SO:0000858 + SO:orthologous_to + orthologous to + The term is sometimes also used for anatomical structures. + in orthology relationship with - Historical homology that involves genes that diverged after a speciation event. + Historical homology that involves genes that diverged after a speciation event. @@ -10864,18 +10867,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - xenologous to - The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). - in xenology relationship with + xenologous to + The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + in xenology relationship with - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. @@ -10888,21 +10891,21 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that involves two members sharing no other homologs in the lineages considered. + Historical homology that involves two members sharing no other homologs in the lineages considered. - 1 to 1 homologous to - 1:1 homology - one-to-one homology - in 1 to 1 homology relationship with + 1 to 1 homologous to + 1:1 homology + one-to-one homology + in 1 to 1 homology relationship with - Historical homology that involves two members sharing no other homologs in the lineages considered. + Historical homology that involves two members sharing no other homologs in the lineages considered. - BGEE:curator + BGEE:curator @@ -10913,19 +10916,19 @@ For example, protein A (transcription factor) indirectly increases by expression - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - 1 to 1 orthologous to - 1:1 orthology - one-to-one orthology - in 1 to 1 orthology relationship with + 1 to 1 orthologous to + 1:1 orthology + one-to-one orthology + in 1 to 1 orthology relationship with - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. @@ -10938,18 +10941,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Paralogy that results from a whole genome duplication event. + Paralogy that results from a whole genome duplication event. - ohnologous to - homoeology - in ohnology relationship with + ohnologous to + homoeology + in ohnology relationship with - Paralogy that results from a whole genome duplication event. + Paralogy that results from a whole genome duplication event. @@ -10962,19 +10965,19 @@ For example, protein A (transcription factor) indirectly increases by expression - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - in-paralogous to - inparalogy - symparalogy - in in-paralogy relationship with + in-paralogous to + inparalogy + symparalogy + in in-paralogy relationship with - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. @@ -10986,19 +10989,19 @@ For example, protein A (transcription factor) indirectly increases by expression - Paralogy that results from a duplication preceding a given speciation event. + Paralogy that results from a duplication preceding a given speciation event. - alloparalogy - out-paralogous to - outparalogy - in out-paralogy relationship with + alloparalogy + out-paralogous to + outparalogy + in out-paralogy relationship with - Paralogy that results from a duplication preceding a given speciation event. + Paralogy that results from a duplication preceding a given speciation event. @@ -11010,17 +11013,17 @@ For example, protein A (transcription factor) indirectly increases by expression - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - pro-orthologous to - in pro-orthology relationship with + pro-orthologous to + in pro-orthology relationship with - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. @@ -11033,18 +11036,18 @@ For example, protein A (transcription factor) indirectly increases by expression - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - semi-orthologous to - The converse of pro-orthologous. - in semi-orthology relationship with + semi-orthologous to + The converse of pro-orthologous. + in semi-orthology relationship with - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. @@ -11057,18 +11060,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Iterative homology that involves structures arranged along the main body axis. + Iterative homology that involves structures arranged along the main body axis. - serial homologous to - homonomy - in serial homology relationship with + serial homologous to + homonomy + in serial homology relationship with - Iterative homology that involves structures arranged along the main body axis. + Iterative homology that involves structures arranged along the main body axis. @@ -11080,20 +11083,20 @@ For example, protein A (transcription factor) indirectly increases by expression - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - heterochronous homologous to - heterochrony - in heterochronous homology relationship with + heterochronous homologous to + heterochrony + in heterochronous homology relationship with - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - ISBN:978-0674639416 + ISBN:978-0674639416 @@ -11104,21 +11107,21 @@ For example, protein A (transcription factor) indirectly increases by expression - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - juvenification - pedomorphosis - in paedomorphorsis relationship with + juvenification + pedomorphosis + in paedomorphorsis relationship with - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - ISBN:978-0674639416 + ISBN:978-0674639416 @@ -11128,16 +11131,16 @@ For example, protein A (transcription factor) indirectly increases by expression - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - in peramorphosis relationship with + in peramorphosis relationship with - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. @@ -11149,19 +11152,19 @@ For example, protein A (transcription factor) indirectly increases by expression - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - in progenesis relationship with + in progenesis relationship with - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - ISBN:978-0674639416 + ISBN:978-0674639416 @@ -11171,21 +11174,21 @@ For example, protein A (transcription factor) indirectly increases by expression - Paedomorphosis that is produced by a retardation of somatic development. + Paedomorphosis that is produced by a retardation of somatic development. - juvenilization - neotenous to - in neoteny relationship with + juvenilization + neotenous to + in neoteny relationship with - Paedomorphosis that is produced by a retardation of somatic development. + Paedomorphosis that is produced by a retardation of somatic development. - ISBN:978-0674639416 + ISBN:978-0674639416 @@ -11195,17 +11198,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Convergence that results from co-evolution usually involving an evolutionary arms race. + Convergence that results from co-evolution usually involving an evolutionary arms race. - mimicrous to - in mimicry relationship with + mimicrous to + in mimicry relationship with - Convergence that results from co-evolution usually involving an evolutionary arms race. + Convergence that results from co-evolution usually involving an evolutionary arms race. @@ -11218,21 +11221,21 @@ For example, protein A (transcription factor) indirectly increases by expression - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - 1 to many orthologous to - 1:many orthology - one-to-many orthology - co-orthology - many to 1 orthology - in 1 to many orthology relationship with + 1 to many orthologous to + 1:many orthology + one-to-many orthology + co-orthology + many to 1 orthology + in 1 to many orthology relationship with - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. @@ -11245,19 +11248,19 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that involves two members of a larger set of homologs. + Historical homology that involves two members of a larger set of homologs. - many to many homologous to - many-to-many homology - many:many homology - in many to many homology relationship with + many to many homologous to + many-to-many homology + many:many homology + in many to many homology relationship with - Historical homology that involves two members of a larger set of homologs. + Historical homology that involves two members of a larger set of homologs. @@ -11269,21 +11272,21 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - 1 to many homologous to - one-to-many homology - 1:many homology - in 1 to many homology relationship with + 1 to many homologous to + one-to-many homology + 1:many homology + in 1 to many homology relationship with - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - BGEE:curator + BGEE:curator @@ -11294,20 +11297,20 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - apomorphous to - synapomorphy - in apomorphy relationship with + apomorphous to + synapomorphy + in apomorphy relationship with - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - ISBN:978-0252068140 + ISBN:978-0252068140 @@ -11317,21 +11320,21 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that is based on distant shared ancestry. + Historical homology that is based on distant shared ancestry. - plesiomorphous to - symplesiomorphy - This term is usually contrasted to apomorphy. - in plesiomorphy relationship with + plesiomorphous to + symplesiomorphy + This term is usually contrasted to apomorphy. + in plesiomorphy relationship with - Historical homology that is based on distant shared ancestry. + Historical homology that is based on distant shared ancestry. - ISBN:978-0252068140 + ISBN:978-0252068140 @@ -11342,21 +11345,21 @@ For example, protein A (transcription factor) indirectly increases by expression - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - deep genetic homology - deep homologous to - generative homology - homoiology - Used for structures in distantly related taxa. - in deep homology relationship with + deep genetic homology + deep homologous to + generative homology + homoiology + Used for structures in distantly related taxa. + in deep homology relationship with - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. @@ -11369,17 +11372,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - hemiplasous to - in hemiplasy relationship with + hemiplasous to + in hemiplasy relationship with - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. @@ -11391,17 +11394,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - gametologous to - in gametology relationship with + gametologous to + in gametology relationship with - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. @@ -11413,20 +11416,20 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - MeSH:Chromosome_Pairing - chromosomal homologous to - in chromosomal homology relationship with + MeSH:Chromosome_Pairing + chromosomal homologous to + in chromosomal homology relationship with - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - ISBN:0195307615 + ISBN:0195307615 @@ -11437,22 +11440,22 @@ For example, protein A (transcription factor) indirectly increases by expression - Orthology that involves two genes that experienced duplications more recent than the species split that created them. + Orthology that involves two genes that experienced duplications more recent than the species split that created them. - many to many orthologous to - many-to-many orthology - many:many orthology - trans-orthology - co-orthology - trans-homology - in many to many orthology relationship with + many to many orthologous to + many-to-many orthology + many:many orthology + trans-orthology + co-orthology + trans-homology + in many to many orthology relationship with - Orthology that involves two genes that experienced duplications more recent than the species split that created them. + Orthology that involves two genes that experienced duplications more recent than the species split that created them. @@ -11466,17 +11469,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Paralogy that involves genes from the same species. + Paralogy that involves genes from the same species. - within-species paralogous to - in within-species paralogy relationship with + within-species paralogous to + in within-species paralogy relationship with - Paralogy that involves genes from the same species. + Paralogy that involves genes from the same species. @@ -11488,18 +11491,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Paralogy that involves genes from different species. + Paralogy that involves genes from different species. - between-species paralogous to - The genes have diverged before a speciation event. - in between-species paralogy relationship with + between-species paralogous to + The genes have diverged before a speciation event. + in between-species paralogy relationship with - Paralogy that involves genes from different species. + Paralogy that involves genes from different species. @@ -11511,17 +11514,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - post-displacement - in postdisplacement relationship with + post-displacement + in postdisplacement relationship with - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. @@ -11533,19 +11536,19 @@ For example, protein A (transcription factor) indirectly increases by expression - Peramorphosis that is produced by a delay in the offset of development. + Peramorphosis that is produced by a delay in the offset of development. - in hypermorphosis relationship with + in hypermorphosis relationship with - Peramorphosis that is produced by a delay in the offset of development. + Peramorphosis that is produced by a delay in the offset of development. - ISBN:978-0674639416 + ISBN:978-0674639416 @@ -11555,17 +11558,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - synologous to - in synology relationship with + synologous to + in synology relationship with - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. @@ -11579,18 +11582,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Orthology that involves functional equivalent genes with retention of the ancestral function. + Orthology that involves functional equivalent genes with retention of the ancestral function. - ECO:0000080 - isoorthologous to - in isoorthology relationship with + ECO:0000080 + isoorthologous to + in isoorthology relationship with - Orthology that involves functional equivalent genes with retention of the ancestral function. + Orthology that involves functional equivalent genes with retention of the ancestral function. @@ -11602,22 +11605,22 @@ For example, protein A (transcription factor) indirectly increases by expression - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - tandem paralogous to - iterative paralogy - serial paralogy - in tandem paralogy relationship with + tandem paralogous to + iterative paralogy + serial paralogy + in tandem paralogy relationship with - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - ISBN:978-0878932665 + ISBN:978-0878932665 @@ -11628,29 +11631,29 @@ For example, protein A (transcription factor) indirectly increases by expression - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - apomorphic tendency - cryptic homology - latent homologous to - underlying synapomorphy - homoiology - homoplastic tendency - re-awakening - Used for structures in closely related taxa. - in latent homology relationship with + apomorphic tendency + cryptic homology + latent homologous to + underlying synapomorphy + homoiology + homoplastic tendency + re-awakening + Used for structures in closely related taxa. + in latent homology relationship with - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - ISBN:0199141118 + ISBN:0199141118 @@ -11660,22 +11663,22 @@ For example, protein A (transcription factor) indirectly increases by expression - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - generative homology - syngenous to - Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. - in syngeny relationship with + generative homology + syngenous to + Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + in syngeny relationship with - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R + DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R @@ -11686,21 +11689,21 @@ For example, protein A (transcription factor) indirectly increases by expression - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - 1:1 paralogy - apparent 1:1 orthology - apparent orthologous to - pseudoorthology - The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. - in apparent orthology relationship with + 1:1 paralogy + apparent 1:1 orthology + apparent orthologous to + pseudoorthology + The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + in apparent orthology relationship with - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. @@ -11713,18 +11716,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - pseudoparalogous to - These genes may come out as paralogs in a single-genome analysis. - in pseudoparalogy relationship with + pseudoparalogous to + These genes may come out as paralogs in a single-genome analysis. + in pseudoparalogy relationship with - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. @@ -11737,18 +11740,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that involves functional equivalent genes with retention of the ancestral function. + Historical homology that involves functional equivalent genes with retention of the ancestral function. - equivalogous to - This may include examples of orthology, paralogy and xenology. - in equivalogy relationship with + equivalogous to + This may include examples of orthology, paralogy and xenology. + in equivalogy relationship with - Historical homology that involves functional equivalent genes with retention of the ancestral function. + Historical homology that involves functional equivalent genes with retention of the ancestral function. @@ -11760,17 +11763,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that involves orthologous pairs of interacting molecules in different organisms. + Historical homology that involves orthologous pairs of interacting molecules in different organisms. - interologous to - in interology relationship with + interologous to + in interology relationship with - Historical homology that involves orthologous pairs of interacting molecules in different organisms. + Historical homology that involves orthologous pairs of interacting molecules in different organisms. @@ -11783,17 +11786,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Similarity that is characterized by interchangeability in function. + Similarity that is characterized by interchangeability in function. - functional similarity - in functional equivalence relationship with + functional similarity + in functional equivalence relationship with - Similarity that is characterized by interchangeability in function. + Similarity that is characterized by interchangeability in function. @@ -11806,17 +11809,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Biological homology that involves parts of the same organism. + Biological homology that involves parts of the same organism. - iterative homologous to - in iterative homology relationship with + iterative homologous to + in iterative homology relationship with - Biological homology that involves parts of the same organism. + Biological homology that involves parts of the same organism. @@ -11828,19 +11831,19 @@ For example, protein A (transcription factor) indirectly increases by expression - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - duplicate xenology - multiple xenology - paraxenologous to - in paraxenology relationship with + duplicate xenology + multiple xenology + paraxenologous to + in paraxenology relationship with - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. @@ -11852,18 +11855,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - plerologous to - This phenomenon is usually due to gene conversion process. - in plerology relationship with + plerologous to + This phenomenon is usually due to gene conversion process. + in plerology relationship with - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. @@ -11876,22 +11879,22 @@ For example, protein A (transcription factor) indirectly increases by expression - Structural homology that involves structures with the same or similar relative positions. + Structural homology that involves structures with the same or similar relative positions. - homotopous to - Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. - in homotopy relationship with + homotopous to + Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + in homotopy relationship with - Structural homology that involves structures with the same or similar relative positions. + Structural homology that involves structures with the same or similar relative positions. - ISBN:0123195837 + ISBN:0123195837 @@ -11901,17 +11904,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Biological homology that involves an ectopic structure and the normally positioned structure. + Biological homology that involves an ectopic structure and the normally positioned structure. - heterotopy - in homeosis relationship with + heterotopy + in homeosis relationship with - Biological homology that involves an ectopic structure and the normally positioned structure. + Biological homology that involves an ectopic structure and the normally positioned structure. @@ -11925,18 +11928,18 @@ For example, protein A (transcription factor) indirectly increases by expression - Synology that results from allopolyploidy. + Synology that results from allopolyploidy. - homoeologous to - On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. - in homoeology relationship with + homoeologous to + On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + in homoeology relationship with - Synology that results from allopolyploidy. + Synology that results from allopolyploidy. @@ -11949,17 +11952,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - axis paramorphism - in paramorphism relationship with + axis paramorphism + in paramorphism relationship with - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. @@ -11972,17 +11975,17 @@ For example, protein A (transcription factor) indirectly increases by expression - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - regulogous to - in regulogy relationship with + regulogous to + in regulogy relationship with - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. @@ -12017,7 +12020,7 @@ For example, protein A (transcription factor) indirectly increases by expression Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - dos + dos 2018-05-22T16:43:28Z This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. has increased age-specific mortality rate @@ -12366,12 +12369,6 @@ For example, protein A (transcription factor) indirectly increases by expression - - - - - - @@ -12522,6 +12519,77 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + ## Elucidation + +This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + +## How to interpret (informal) + +First the &quot;atemporal&quot; FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + axiom holds for all times + + + + + + + + ## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y) + relation has no temporal argument + + + + + diff --git a/ro-full.json b/ro-full.json new file mode 100644 index 00000000..34cbf834 --- /dev/null +++ b/ro-full.json @@ -0,0 +1,18127 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/ro-full.json", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/description", + "val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." + }, { + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "OBO Relations Ontology" + }, { + "pred" : "http://purl.org/dc/terms/license", + "val" : "https://creativecommons.org/publicdomain/zero/1.0/" + }, { + "pred" : "http://www.w3.org/2002/07/owl#versionInfo", + "val" : "2023-02-19" + }, { + "pred" : "http://xmlns.com/foaf/0.1/homepage", + "val" : " https://github.com/oborel/obo-relations/" + } ], + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-19/ro-full.json" + }, + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "lbl" : "continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "lbl" : "occurrent", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "lbl" : "independent continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000006", + "lbl" : "spatial region", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "lbl" : "process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "lbl" : "disposition", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "lbl" : "realizable entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "lbl" : "quality", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "lbl" : "specifically dependent continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "lbl" : "role", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "lbl" : "generically dependent continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "lbl" : "function", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "lbl" : "material entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease is realized in this disease course" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is realized in this shattering" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is realized in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is realized by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "realized_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realizes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease course realizes this disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation realizes this investigator role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this shattering realizes this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000060", + "lbl" : "obsolete preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occurs_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "site of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000141", + "lbl" : "immaterial entity", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000000", + "lbl" : "anatomical entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", + "xrefs" : [ "CAROC:Brownsville2014" ] + }, + "comments" : [ "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000003", + "lbl" : "connected anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." + }, + "comments" : [ "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000006", + "lbl" : "material anatomical entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical entity that has mass." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000007", + "lbl" : "immaterial anatomical entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical entity that has no mass." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001001", + "lbl" : "neuron projection bundle", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001010", + "lbl" : "organism or virus or viroid", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Melissa Haendel" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0010000", + "lbl" : "multicellular anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical structure that has more than one cell as a part." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "djs93" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000000", + "lbl" : "cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", + "xrefs" : [ "CARO:mah" ] + }, + "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], + "xrefs" : [ { + "val" : "CALOHA:TS-2035" + }, { + "val" : "FBbt:00007002" + }, { + "val" : "FMA:68646" + }, { + "val" : "GO:0005623" + }, { + "val" : "KUPO:0000002" + }, { + "val" : "MESH:D002477" + }, { + "val" : "VHOG:0001533" + }, { + "val" : "WBbt:0004017" + }, { + "val" : "XAO:0003012" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000101", + "lbl" : "sensory neuron", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any neuron having a sensory function; an afferent neuron conveying sensory impulses.", + "xrefs" : [ "ISBN:0721662544" ] + }, + "xrefs" : [ { + "val" : "BTO:0001037" + }, { + "val" : "FBbt:00005124" + }, { + "val" : "FMA:84649" + }, { + "val" : "MESH:D011984" + }, { + "val" : "WBbt:0005759" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0000540", + "lbl" : "neuron", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.", + "xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ] + }, + "comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "nerve cell" + } ], + "xrefs" : [ { + "val" : "BTO:0000938" + }, { + "val" : "CALOHA:TS-0683" + }, { + "val" : "FBbt:00005106" + }, { + "val" : "FMA:54527" + }, { + "val" : "VHOG:0001483" + }, { + "val" : "WBbt:0003679" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", + "lbl" : "environmental system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A system which has the disposition to environ one or more material entities.", + "xrefs" : [ "DOI:10.1186/2041-1480-4-43" ] + }, + "comments" : [ "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "environment" + } ], + "xrefs" : [ { + "val" : "EcoLexicon:environment" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-09-23T16:04:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01003004", + "lbl" : "derives from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0003674", + "lbl" : "molecular_function", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", + "xrefs" : [ "GOC:pdt" ] + }, + "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecular function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0004842", + "lbl" : "ubiquitin-protein transferase activity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.", + "xrefs" : [ "GOC:BioGRID", "GOC:jh2", "PMID:9635407" ] + }, + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "anaphase-promoting complex activity", + "xrefs" : [ "GOC:dph", "GOC:tb" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "ubiquitin conjugating enzyme activity" + }, { + "pred" : "hasNarrowSynonym", + "val" : "ubiquitin ligase activity" + }, { + "pred" : "hasNarrowSynonym", + "val" : "ubiquitin protein ligase activity" + }, { + "pred" : "hasNarrowSynonym", + "val" : "ubiquitin protein-ligase activity" + }, { + "pred" : "hasNarrowSynonym", + "val" : "ubiquitin-conjugating enzyme activity" + }, { + "pred" : "hasRelatedSynonym", + "val" : "E2" + }, { + "pred" : "hasRelatedSynonym", + "val" : "E3" + } ], + "xrefs" : [ { + "val" : "KEGG_REACTION:R03876" + }, { + "val" : "Reactome:R-HSA-1169394" + }, { + "val" : "Reactome:R-HSA-1169395" + }, { + "val" : "Reactome:R-HSA-1169397" + }, { + "val" : "Reactome:R-HSA-1169398" + }, { + "val" : "Reactome:R-HSA-1169402" + }, { + "val" : "Reactome:R-HSA-1169405" + }, { + "val" : "Reactome:R-HSA-1169406" + }, { + "val" : "Reactome:R-HSA-1234163" + }, { + "val" : "Reactome:R-HSA-1234172" + }, { + "val" : "Reactome:R-HSA-1253282" + }, { + "val" : "Reactome:R-HSA-1358789" + }, { + "val" : "Reactome:R-HSA-1358790" + }, { + "val" : "Reactome:R-HSA-1358792" + }, { + "val" : "Reactome:R-HSA-1363331" + }, { + "val" : "Reactome:R-HSA-168915" + }, { + "val" : "Reactome:R-HSA-173542" + }, { + "val" : "Reactome:R-HSA-173545" + 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"id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002134", + "lbl" : "innervates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that ( some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "lbl" : "derived by descent from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral_stucture_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "evolutionarily_descended_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "lbl" : "has derived by descendant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of derived by descent from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "lbl" : "serially homologous to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + }, + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9227-417X" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002171", + "lbl" : "mutually spatially disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "non-overlapping with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no parts with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX owl: \nPREFIX part_of: \nPREFIX mutually_spatially_disjoint_with: \nCONSTRUCT {\n part_of: a owl:ObjectProperty .\n [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?x ;\n owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?y\n ]\n ]\n}\nWHERE {\n ?x mutually_spatially_disjoint_with: ?y .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/RO_0002163" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002172", + "lbl" : "taxonomic class assertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002173", + "lbl" : "ambiguous for taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002174", + "lbl" : "dubious for taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T." + }, + "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" + }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002204", + "lbl" : "gene product of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "lbl" : "has gene product", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002214", + "lbl" : "has prototype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002217", + "lbl" : "obsolete actively participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" + }, + "comments" : [ "Obsoleted as the inverse property was obsoleted." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "agent in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002608" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002218", + "lbl" : "obsolete has active participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has agent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002500" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Allen" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ends with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "finished by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002245", + "lbl" : "over-expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002246", + "lbl" : "under-expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "lbl" : "defined by inverse", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002291", + "lbl" : "ubiquitously expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'expressed in'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002293", + "lbl" : "ubiquitously expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ubiquiotously expressed in" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002310", + "lbl" : "exposure event or process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:55:39Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/173" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002312", + "lbl" : "evolutionary variant of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002345", + "lbl" : "exports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002348", + "lbl" : "results in commitment to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002349", + "lbl" : "results in determination of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "lbl" : "member of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "is member of is a mereological relation between a item and a collection." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An organism that is a member of a population of organisms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is member of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "member part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "lbl" : "has member", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "lbl" : "input of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has input" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "lbl" : "output of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has output" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "lbl" : "formed as result of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002355", + "lbl" : "results in structural organization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002356", + "lbl" : "results in specification of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002374", + "lbl" : "derived from ancestral fusion of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" + }, + "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "has fused element" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002401", + "lbl" : "obsolete has indirect input", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002402", + "lbl" : "obsolete has direct output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "translation SubClassOf has_direct_output some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly produces" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002403", + "lbl" : "obsolete has indirect output", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002406", + "lbl" : "obsolete directly activates", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002629" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002408", + "lbl" : "obsolete directly inhibits", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002630" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002416", + "lbl" : "logical macro assertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002419", + "lbl" : "annotation property cardinality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002420", + "lbl" : "logical macro assertion on a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a class" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002421", + "lbl" : "logical macro assertion on a property", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a property" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002422", + "lbl" : "logical macro assertion on an object property", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "lbl" : "logical macro assertion on an annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002424", + "lbl" : "differs in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This is an exploratory relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002425", + "lbl" : "differs in attribute of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "lbl" : "differs in attribute", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000316" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0208" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "lbl" : "molecularly interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "binds" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "molecularly binds with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0915" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002437", + "lbl" : "biotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "interacts with on organism level" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/interactsWith" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002438", + "lbl" : "trophically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the partners are related via a feeding relationship." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "lbl" : "preys on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Baleen whale preys on krill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7134-3324" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of predation interaction with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preys upon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/preysUpon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.inaturalist.org/observations/2942824" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002440", + "lbl" : "symbiotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction in which the two organisms live together in more or less intimate association." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002441", + "lbl" : "commensually interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002442", + "lbl" : "mutualistically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "lbl" : "interacts with via parasite-host interaction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002444", + "lbl" : "parasite of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "direct parasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Pediculus humanus capitis parasite of human" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitizes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/parasitizes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002445", + "lbl" : "parasitized by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "directly parasitized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "semibiotically interacts with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Porifiera attaches to substrate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002447", + "lbl" : "phosphorylates", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "lbl" : "directly regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly decreases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly inhibits" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "lbl" : "directly positively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly increases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly activates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002451", + "lbl" : "transmitted by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a disease and organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "all dengue disease transmitted by some mosquito" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Add domain and range constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002452", + "lbl" : "has symptom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between a disease or an organism and a phenotype" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002453", + "lbl" : "host of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "lbl" : "has host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasHost" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002455", + "lbl" : "pollinates", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Bees pollinate Flowers" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/pollinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "lbl" : "pollinated by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has polinator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasPollinator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "lbl" : "acquires nutrients from", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002458", + "lbl" : "preyed upon by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of preys on" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has predator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of predation interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/HasPredator" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "lbl" : "is vector for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002460", + "lbl" : "has vector", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002461", + "lbl" : "partner in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002462", + "lbl" : "subject participant in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002464", + "lbl" : "helper property (not for use in curation)", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002465", + "lbl" : "is symbiosis", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002466", + "lbl" : "is commensalism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002467", + "lbl" : "is mutualism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002468", + "lbl" : "is parasitism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002472", + "lbl" : "is evidence for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002474", + "lbl" : "dispositional interpretation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002475", + "lbl" : "has no connections with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no connection with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002481", + "lbl" : "is kinase activity", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002482", + "lbl" : "is ubiquitination", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002483", + "lbl" : "inherited annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002484", + "lbl" : "curator guidance link", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "exists during" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/BFO_0000169" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002503", + "lbl" : "towards", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002504", + "lbl" : "always present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brain always_present_in_taxon 'Vertebrata'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "forelimb always_present_in_taxon Euarchontoglires" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "never lost in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002505", + "lbl" : "has intermediate", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has intermediate product" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002506", + "lbl" : "causal relation between entities", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002507", + "lbl" : "determined by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A coral reef environment is determined by a particular coral reef" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/24330602" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determined by (system to material entity)" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002508", + "lbl" : "determines", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of determined by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determines (material entity to system)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002509", + "lbl" : "determined by part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002510", + "lbl" : "transcribed from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is transcribed from y if and only if x is synthesized from template y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002511", + "lbl" : "transcribed to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of transcribed from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002512", + "lbl" : "ribosomal translation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002513", + "lbl" : "ribosomally translates to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ribosomal translation of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002514", + "lbl" : "sequentially related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are sequentially adjacent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002516", + "lbl" : "has start sequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002518", + "lbl" : "has end sequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ended by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002519", + "lbl" : "is end sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has end sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002520", + "lbl" : "is consecutive sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the SO paper, this was defined as an instance-type relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002521", + "lbl" : "is sequentially aligned with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "lbl" : "bounds sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002523", + "lbl" : "is bound by sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of bounds sequence of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "lbl" : "has subsequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contains" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "lbl" : "is subsequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has subsequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained by" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "lbl" : "overlaps sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002527", + "lbl" : "does not overlap sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "disconnected from" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "lbl" : "is upstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of downstream of sequence of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "lbl" : "is downstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002530", + "lbl" : "is immediately downstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002529" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002531", + "lbl" : "is immediately upstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of immediately downstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002532", + "lbl" : "sequentially ordered entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any entity that is ordered in discrete units along a linear axis." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002533", + "lbl" : "sequence atomic unit", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any individual unit of a collection of like units arranged in a linear order" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002534", + "lbl" : "sequence bearer", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any entity that can be divided into parts such that each part is an atomical unit of a sequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002535", + "lbl" : "temporal logical macro assertion on a class", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002536", + "lbl" : "measurement property has unit", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002537", + "lbl" : "has start time value", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002538", + "lbl" : "has end time value", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002539", + "lbl" : "start, days post fertilization", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002540", + "lbl" : "end, days post fertilization", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002541", + "lbl" : "start, years post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002542", + "lbl" : "end, years post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002543", + "lbl" : "start, months post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002544", + "lbl" : "end, months post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002545", + "lbl" : "month of gestation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002546", + "lbl" : "has developmental stage marker", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002547", + "lbl" : "start, days post coitum", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of coitum." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002548", + "lbl" : "end, days post coitum", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the end of the stage and the time of coitum." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002549", + "lbl" : "start, weeks post birth", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002550", + "lbl" : "end, weeks post birth", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002551", + "lbl" : "has skeleton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has supporting framework" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002552", + "lbl" : "results in ending of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002553", + "lbl" : "hyperparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "hyperparasitoid of" + }, { + "pred" : "hasRelatedSynonym", + "val" : "epiparasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://eol.org/schema/terms/hyperparasitoidOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Hyperparasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "lbl" : "hyperparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of hyperparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "has epiparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has hyperparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hyperparasitoidized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002555", + "lbl" : "allelopath of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Allelopathy" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/allelopathyYes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002556", + "lbl" : "pathogen of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002557", + "lbl" : "has pathogen", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002558", + "lbl" : "has evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of is evidence for" + }, + "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/25052702" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "lbl" : "causally influenced by", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influenced by (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002560", + "lbl" : "is asymmetric relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002561", + "lbl" : "is symmetric relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002562", + "lbl" : "is relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "lbl" : "interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "lbl" : "molecular interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002565", + "lbl" : "results in movement of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "lbl" : "causally influences", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "lbl" : "biomechanically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002568", + "lbl" : "has muscle antagonist", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Antagonist_(muscle)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002569", + "lbl" : "has branching part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of branching part of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "lbl" : "conduit for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "UBERON:cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002571", + "lbl" : "lumen of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:cjm" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002572", + "lbl" : "luminal space of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002573", + "lbl" : "has modifier", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between an attribute or a qualifier and another attribute." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002574", + "lbl" : "participates in a biotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002575", + "lbl" : "is direct form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002423", + "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "lbl" : "skeleton of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has skeleton" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002577", + "lbl" : "system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A material entity consisting of multiple components that are causally integrated." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.jbiomedsem.com/content/4/1/43" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "lbl" : "directly regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002579", + "lbl" : "is indirect form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002580", + "lbl" : "logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002581", + "lbl" : "is a defining property chain axiom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002583", + "lbl" : "existence starts at end of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002584", + "lbl" : "has part structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002585", + "lbl" : "results in closure of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002586", + "lbl" : "results in breakdown of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002587", + "lbl" : "results in synthesis of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002588", + "lbl" : "results in assembly of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002589", + "lbl" : "results in catabolism of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002590", + "lbl" : "results in disassembly of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002591", + "lbl" : "results in remodeling of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002592", + "lbl" : "results in organization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002593", + "lbl" : "existence ends at start of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002594", + "lbl" : "is relational form of a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "lbl" : "causal relation between material entity and a process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002596", + "lbl" : "capable of regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pyrethroid -> growth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "lbl" : "capable of negatively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "lbl" : "capable of positively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "renin -> arteriolar smooth muscle contraction" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002599", + "lbl" : "capable of inhibiting or preventing pathological process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pazopanib -> pathological angiogenesis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002600", + "lbl" : "capable of upregulating or causing pathological process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "benzene -> cancer [CHEBI]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "causes disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002601", + "lbl" : "logical macro assertion involving identity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A shortcut relationship that holds between two entities based on their identity criteria" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002602", + "lbl" : "in approximate one to one relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002603", + "lbl" : "is approximately equivalent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002604", + "lbl" : "is opposite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002605", + "lbl" : "is indistinguishable from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002606", + "lbl" : "is substance that treats", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002607", + "lbl" : "is marker for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be ceded to OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002608", + "lbl" : "process has causal agent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'causal agent in process'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002609", + "lbl" : "obsolete related via dependence to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002610", + "lbl" : "correlated with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Groups both positive and negative correlation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002611", + "lbl" : "evidential logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002612", + "lbl" : "axiom has evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002613", + "lbl" : "axiom contradicted by evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002614", + "lbl" : "is evidence with support from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." + }, + "comments" : [ "In the Gene Ontology association model, this corresponds to the With/From field" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002615", + "lbl" : "has model", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of is-model-of" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002616", + "lbl" : "related via evidence or inference to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002617", + "lbl" : "is representative IRI for equivalence set", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002618", + "lbl" : "visits", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/74" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002619", + "lbl" : "visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002622", + "lbl" : "visits flowers of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002623", + "lbl" : "has flowers visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002624", + "lbl" : "lays eggs in", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002625", + "lbl" : "has eggs laid in by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002626", + "lbl" : "kills", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://github.com/jhpoelen/eol-globi-data/issues/143" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002627", + "lbl" : "is killed by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "lbl" : "directly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002630", + "lbl" : "directly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002632", + "lbl" : "ectoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002633", + "lbl" : "has ectoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ectoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002634", + "lbl" : "endoparasite of", + "type" : "PROPERTY", + "meta" : { + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "lives inside of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002635", + "lbl" : "has endoparasite", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002636", + "lbl" : "mesoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002637", + "lbl" : "has mesoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of mesoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002638", + "lbl" : "intercellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002639", + "lbl" : "has intercellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intercellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002640", + "lbl" : "intracellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002641", + "lbl" : "has intracellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intracellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002801", + "lbl" : "co-roosts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Communal_roosting" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003000", + "lbl" : "produces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." + }, + "comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "lbl" : "produced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a produced_by b iff some process that occurs_in b has_output a." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003002", + "lbl" : "represses expression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003003", + "lbl" : "increases expression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "lbl" : "has role in modeling", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." + }, + "comments" : [ "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-1048-5019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is used to study" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "lbl" : "causes or contributes to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." + }, + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003303", + "lbl" : "causes condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "lbl" : "contributes to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "lbl" : "contributes to severity of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to expressivity of condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003306", + "lbl" : "contributes to frequency of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to penetrance of condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "lbl" : "ameliorates condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." + }, + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preventative for condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003308", + "lbl" : "correlated with condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003309", + "lbl" : "exacerbates condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003310", + "lbl" : "condition ameliorated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003311", + "lbl" : "condition exacerbated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004000", + "lbl" : "condition has genetic basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:38:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004001", + "lbl" : "has material basis in gain of function germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:20Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410295" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410296" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004002", + "lbl" : "has material basis in loss of function germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004003", + "lbl" : "has material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:54Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004004", + "lbl" : "has material basis in somatic mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:07Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004005", + "lbl" : "has major susceptibility factor", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:26Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004006", + "lbl" : "has partial material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:57Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004007", + "lbl" : "has primary input or output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : 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goal of process is to modify, consume, or transform c.", + "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:56Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004010", + "lbl" : "is genetic basis for condition", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:53:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004011", + "lbl" : "is causal gain of function germline mutation of in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : 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"http://purl.obolibrary.org/obo/RO_0004013", + "lbl" : "is causal germline mutation in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:56:40Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004014", + "lbl" : "is causal somatic mutation in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:57:07Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004015", + "lbl" : "is causal susceptibility factor for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:57:43Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317345" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004016", + "lbl" : "is causal germline mutation partially giving rise to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:58:43Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317346" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004017", + "lbl" : "realizable has basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:01Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004018", + "lbl" : "is basis for realizable", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004019", + "lbl" : "disease has basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:26:47Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004020", + "lbl" : "disease has basis in dysfunction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in dysfunction of (disease to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:29:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004021", + "lbl" : "disease has basis in disruption of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:37:52Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004022", + "lbl" : "disease has basis in feature", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:46:07Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004023", + "lbl" : "causal relationship with disease as subject", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:50:54Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004024", + "lbl" : "disease causes disruption of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:51:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004025", + "lbl" : "disease causes dysfunction of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes dysfunction of (disease to anatomical entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:58:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004026", + "lbl" : "disease has location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T04:06:02Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004027", + "lbl" : "disease has inflammation site", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:37:31Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004029", + "lbl" : "disease has feature", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:50:53Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "lbl" : "disease arises from alteration in structure", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "lbl" : "enables subfunction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-25T23:20:13Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "lbl" : "acts upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:30Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "lbl" : "acts upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:51Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "lbl" : "acts upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "lbl" : "acts upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004036", + "lbl" : "nominally disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004048", + "lbl" : "is directional form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:59:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004049", + "lbl" : "is positive form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:16Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004096", + "lbl" : "DEPRECATED inheres in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004097", + "lbl" : "DEPRECATED bearer of", + "type" : "PROPERTY", + "meta" : { + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007000", + "lbl" : "has driver", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007001", + "lbl" : "has disease driver", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008501", + "lbl" : "epiphyte of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Epiphyte" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008502", + "lbl" : "has epiphyte", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of epiphyte of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008503", + "lbl" : "kleptoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008504", + "lbl" : "kleptoparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of kleptoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008505", + "lbl" : "creates habitat for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008506", + "lbl" : "ecologically co-occurs with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008507", + "lbl" : "lays eggs on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008508", + "lbl" : "has eggs laid on by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of lays eggs on" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009001", + "lbl" : "has substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "muffin 'has substance added' some 'baking soda'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009002", + "lbl" : "has substance removed", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'egg white' 'has substance removed' some 'egg yolk'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009003", + "lbl" : "immersed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardines 'immersed in' some 'oil and mustard'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009004", + "lbl" : "has consumer", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardine has consumer some homo sapiens" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009005", + "lbl" : "has primary substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bread 'has primary substance added' some 'flour'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "lbl" : "realized in response to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "triggered by process", + "xrefs" : [ "RO:cjm" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "lbl" : "generically depends on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "g-depends on" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Genetic information generically depend on molecules of DNA." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The novel *War and Peace* generically depends on this copy of the novel." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The pattern shared by chess boards generically depends on any chess board." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The score of a symphony g-depends on a copy of the score." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This pdf file generically depends on this server." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "[072-ISO]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0010002", + "lbl" : "is carrier of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Molecules of DNA are carriers of genetic information." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This copy of *War and Peace* is carrier of the novel written by Tolstoy." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "This hard drive is carrier of these data items." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "[072-ISO]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011002", + "lbl" : "regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011003", + "lbl" : "regulates quantity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011004", + "lbl" : "indirectly regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011007", + "lbl" : "decreases by repression quantity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011008", + "lbl" : "increases by expression quantity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011009", + "lbl" : "directly positively regulates quantity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A has an activity that directly positively regulates the quantity of B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011010", + "lbl" : "directly negatively regulates quantity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A has an activity that directly negatively regulates the quantity of B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011013", + "lbl" : "indirectly positively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011014", + "lbl" : "destabilizes quantity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0011015", + "lbl" : "stabilizes quantity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "AKT1 stabilizes quantity of 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Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "lbl" : "decreased in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015009", + "lbl" : "similar in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "lbl" : "has relative magnitude", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015011", + "lbl" : "has cross section", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015012", + "lbl" : "reciprocal of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015015", + "lbl" : "has high plasma membrane amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "lbl" : "has low plasma membrane amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016001", + "lbl" : "has phenotype or disease", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016002", + "lbl" : "has disease", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:44Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016004", + "lbl" : "has exposure medium", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000083" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-12-14T20:41:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7463-6306" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017001", + "lbl" : "device utilizes material", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "utilizes" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A diagnostic testing device utilizes a specimen." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-2620-0345" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-11-08T12:00:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018001", + "lbl" : "is myristoyltransferase activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Helper relation for OWL definition of RO:0018002 myristoylates" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018002", + "lbl" : "myristoylates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/conformsTo", + "val" : "http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018003", + "lbl" : "myristoylated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of myristoylates" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018027", + "lbl" : "is agonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P3772" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018028", + "lbl" : "is inverse agonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P9275" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018029", + "lbl" : "is antagonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P3773" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0019000", + "lbl" : "regulates characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0019001", + "lbl" : "positively regulates characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0019002", + "lbl" : "negatively regulates characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0019501", + "lbl" : "confers susceptibility to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-4142-7153" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0040035", + "lbl" : "disease relationship", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relation groups relations between diseases and any other kind of entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T00:00:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0040036", + "lbl" : "results in changes to anatomical or cellular structure", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has anatomical participant c iff p has participant c, and c is an anatomical entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T01:08:58Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0040042", + "lbl" : "is homeomorphic for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C." + }, + "comments" : [ "R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "part-of is homeomorphic for independent continuants." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-10-21T19:46:34Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/164" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "lbl" : "in similarity relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000000", "BGEE:curator" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "sameness" + }, { + "pred" : "hasExactSynonym", + "val" : "similar to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "correspondence", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "resemblance" + } ], + "xrefs" : [ { + "val" : "ECO:0000041" + }, { + "val" : "SO:similar_to" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000000" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000001", + "lbl" : "in homology relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Similarity that results from common evolutionary origin.", + "xrefs" : [ "http://dx.doi.org/10.1002/bies.950180611", "http://dx.doi.org/10.1002/jmor.1051730307", "http://dx.doi.org/10.1007/BF02814480", "http://purl.obolibrary.org/obo/HOM_0000001" ] + }, + "comments" : [ "This broad definition encompasses all the working definitions proposed so far in the literature." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homologous to" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000001" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000002", + "lbl" : "in homoplasy relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Similarity that results from independent evolution.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000002" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homoplasous to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "analogy" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000002" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000003", + "lbl" : "in homocracy relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814484", "http://dx.doi.org/10.1007/s00427-003-0301-4", "http://dx.doi.org/10.1186/1742-9994-2-15", "http://purl.obolibrary.org/obo/HOM_0000003" ] + }, + "comments" : [ "Homology and homocracy are not mutually exclusive. 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"predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004024", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013002", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013003", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013003", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013007", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0015001", "http://purl.obolibrary.org/obo/RO_0015003" ] + } ] + } ] +} \ No newline at end of file diff --git a/ro-full.obo b/ro-full.obo new file mode 100644 index 00000000..b874c5f3 --- /dev/null +++ b/ro-full.obo @@ -0,0 +1,7082 @@ +format-version: 1.2 +data-version: ro/releases/2023-02-19/ro-full.owl +subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" +subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" +subsetdef: ro-eco "" +subsetdef: RO:0002259 "" +ontology: ro/ro-full +property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string +property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ +property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI +property_value: owl:versionInfo "2023-02-19" xsd:string + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +disjoint_from: BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant +relationship: RO:0002214 BFO:0000002 {all_only="true"} ! has prototype continuant +relationship: RO:HOM0000000 BFO:0000002 {all_only="true"} ! continuant + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent +relationship: RO:HOM0000000 BFO:0000003 {all_only="true"} ! occurrent + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant + +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +is_a: BFO:0000003 ! occurrent +relationship: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process + +[Term] +id: BFO:0000016 +name: disposition +is_a: BFO:0000017 ! realizable entity +disjoint_from: BFO:0000023 ! role + +[Term] +id: BFO:0000017 +name: realizable entity +def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] +is_a: BFO:0000020 ! specifically dependent continuant +disjoint_from: BFO:0000019 ! quality +relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant + +[Term] +id: BFO:0000023 +name: role +def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] +is_a: BFO:0000017 ! realizable entity + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] +is_a: BFO:0000002 ! continuant +relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant + +[Term] +id: BFO:0000034 +name: function +is_a: BFO:0000016 ! disposition + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant +disjoint_from: BFO:0000141 ! immaterial entity + +[Term] +id: BFO:0000141 +name: immaterial entity +is_a: BFO:0000004 ! independent continuant + +[Term] +id: CARO:0000000 +name: anatomical entity +def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [CAROC:Brownsville2014] +comment: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. +is_a: BFO:0000004 ! independent continuant + +[Term] +id: CARO:0000003 +name: connected anatomical structure +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [] +comment: Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. +is_a: CARO:0000006 ! material anatomical entity + +[Term] +id: CARO:0000006 +name: material anatomical entity +def: "An anatomical entity that has mass." [] +is_a: CARO:0000000 ! anatomical entity +disjoint_from: CARO:0000007 ! immaterial anatomical entity + +[Term] +id: CARO:0000007 +name: immaterial anatomical entity +def: "Anatomical entity that has no mass." [] +is_a: BFO:0000141 ! immaterial entity +is_a: CARO:0000000 ! anatomical entity + +[Term] +id: CARO:0001001 +name: neuron projection bundle +def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [] +is_a: CARO:0000006 ! material anatomical entity + +[Term] +id: CARO:0001010 +name: organism or virus or viroid +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000117 "Melissa Haendel" xsd:string + +[Term] +id: CARO:0010000 +name: multicellular anatomical structure +def: "An anatomical structure that has more than one cell as a part." [] +is_a: CARO:0000003 ! connected anatomical structure +property_value: IAO:0000117 "djs93" xsd:string + +[Term] +id: CHEBI:50906 +is_a: PATO:0000001 ! quality + +[Term] +id: CL:0000000 +name: cell +def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] +comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). +xref: CALOHA:TS-2035 +xref: FBbt:00007002 +xref: FMA:68646 +xref: GO:0005623 +xref: KUPO:0000002 +xref: MESH:D002477 +xref: VHOG:0001533 +xref: WBbt:0004017 +xref: XAO:0003012 + +[Term] +id: CL:0000101 +name: sensory neuron +def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] +xref: BTO:0001037 +xref: FBbt:00005124 +xref: FMA:84649 +xref: MESH:D011984 +xref: WBbt:0005759 +is_a: CL:0000540 ! neuron + +[Term] +id: CL:0000540 +name: neuron +def: "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [http://en.wikipedia.org/wiki/Neuron, MESH:D009474] +comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. +synonym: "nerve cell" EXACT [] +xref: BTO:0000938 +xref: CALOHA:TS-0683 +xref: FBbt:00005106 +xref: FMA:54527 +xref: VHOG:0001483 +xref: WBbt:0003679 +is_a: BFO:0000040 ! material entity +is_a: CL:0000000 ! cell +property_value: RO:0002175 NCBITaxon:9606 + +[Term] +id: ENVO:01000254 +name: environmental system +def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +synonym: "environment" EXACT [] +xref: EcoLexicon:environment +is_a: RO:0002577 ! system +creation_date: 2013-09-23T16:04:08Z + +[Term] +id: GO:0003674 +name: molecular_function +def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt] +comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +synonym: "molecular function" EXACT [] + +[Term] +id: GO:0004842 +name: ubiquitin-protein transferase activity +def: "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." [GOC:BioGRID, GOC:jh2, PMID:9635407] +synonym: "anaphase-promoting complex activity" NARROW [GOC:dph, GOC:tb] +synonym: "E2" RELATED [] +synonym: "E3" RELATED [] +synonym: "ubiquitin conjugating enzyme activity" NARROW [] +synonym: "ubiquitin ligase activity" NARROW [] +synonym: "ubiquitin protein ligase activity" NARROW [] +synonym: "ubiquitin protein-ligase activity" NARROW [] +synonym: "ubiquitin-conjugating enzyme activity" NARROW [] +xref: KEGG_REACTION:R03876 +xref: Reactome:R-HSA-1169394 "ISGylation of IRF3" +xref: Reactome:R-HSA-1169395 "ISGylation of viral protein NS1" +xref: Reactome:R-HSA-1169397 "Activation of ISG15 by UBA7 E1 ligase" +xref: Reactome:R-HSA-1169398 "ISGylation of host protein filamin B" +xref: Reactome:R-HSA-1169402 "ISGylation of E2 conjugating enzymes" +xref: Reactome:R-HSA-1169405 "ISGylation of protein phosphatase 1 beta (PP2CB)" +xref: Reactome:R-HSA-1169406 "ISGylation of host proteins" +xref: Reactome:R-HSA-1234163 "Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha" +xref: Reactome:R-HSA-1234172 "Nuclear VBC complex ubiquitinylates HIF-alpha" +xref: Reactome:R-HSA-1253282 "ERBB4 ubiquitination by WWP1/ITCH" +xref: Reactome:R-HSA-1358789 "Self-ubiquitination of RNF41" +xref: Reactome:R-HSA-1358790 "RNF41 ubiquitinates ERBB3" +xref: Reactome:R-HSA-1358792 "RNF41 ubiquitinates activated ERBB3" +xref: Reactome:R-HSA-1363331 "Ubiquitination of p130 (RBL2) by SCF (Skp2)" +xref: Reactome:R-HSA-168915 "K63-linked ubiquitination of RIP1 bound to the activated TLR complex" +xref: Reactome:R-HSA-173542 "SMURF2 ubiquitinates SMAD2" +xref: Reactome:R-HSA-173545 "Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling" +xref: Reactome:R-HSA-174057 "Multiubiquitination of APC/C-associated Cdh1" +xref: Reactome:R-HSA-174104 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex" +xref: Reactome:R-HSA-174144 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex" +xref: Reactome:R-HSA-174159 "Ubiquitination of Emi1 by SCF-beta-TrCP" +xref: Reactome:R-HSA-174195 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex" +xref: Reactome:R-HSA-174227 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex" +xref: Reactome:R-HSA-179417 "Multiubiquitination of Nek2A" +xref: Reactome:R-HSA-180540 "Multi-ubiquitination of APOBEC3G" +xref: Reactome:R-HSA-180597 "Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex" +xref: Reactome:R-HSA-182986 "CBL-mediated ubiquitination of CIN85" +xref: Reactome:R-HSA-182993 "Ubiquitination of stimulated EGFR (CBL)" +xref: Reactome:R-HSA-183036 "Ubiquitination of stimulated EGFR (CBL:GRB2)" +xref: Reactome:R-HSA-183051 "CBL ubiquitinates Sprouty" +xref: Reactome:R-HSA-183084 "CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix" +xref: Reactome:R-HSA-183089 "CBL binds and ubiquitinates phosphorylated Sprouty" +xref: Reactome:R-HSA-1852623 "Ubiquitination of NICD1 by FBWX7" +xref: Reactome:R-HSA-187575 "Ubiquitination of phospho-p27/p21" +xref: Reactome:R-HSA-1912357 "ITCH ubiquitinates DTX" +xref: Reactome:R-HSA-1912386 "Ubiquitination of NOTCH1 by ITCH in the absence of ligand" +xref: Reactome:R-HSA-1918092 "CHIP (STUB1) mediates ubiquitination of ERBB2" +xref: Reactome:R-HSA-1918095 "CUL5 mediates ubiquitination of ERBB2" +xref: Reactome:R-HSA-1977296 "NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer" +xref: Reactome:R-HSA-1980074 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1" +xref: Reactome:R-HSA-1980118 "ARRB mediates NOTCH1 ubiquitination" +xref: Reactome:R-HSA-201425 "Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling" +xref: Reactome:R-HSA-202453 "Auto-ubiquitination of TRAF6" +xref: Reactome:R-HSA-202534 "Ubiquitination of NEMO by TRAF6" +xref: Reactome:R-HSA-205118 "TRAF6 polyubiquitinates NRIF" +xref: Reactome:R-HSA-209063 "Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex" +xref: Reactome:R-HSA-211734 "Ubiquitination of PAK-2p34" +xref: Reactome:R-HSA-2169050 "SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7" +xref: Reactome:R-HSA-2172172 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH2" +xref: Reactome:R-HSA-2179276 "SMURF2 monoubiquitinates SMAD3" +xref: Reactome:R-HSA-2186747 "Ubiquitination of SKI/SKIL by RNF111/SMURF2" +xref: Reactome:R-HSA-2186785 "RNF111 ubiquitinates SMAD7" +xref: Reactome:R-HSA-2187368 "STUB1 (CHIP) ubiquitinates SMAD3" +xref: Reactome:R-HSA-2213017 "Auto-ubiquitination of TRAF3" +xref: Reactome:R-HSA-264444 "Autoubiquitination of phospho-COP1(Ser-387 )" +xref: Reactome:R-HSA-2682349 "RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels" +xref: Reactome:R-HSA-2730904 "Auto-ubiquitination of TRAF6" +xref: Reactome:R-HSA-2737728 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants" +xref: Reactome:R-HSA-2769007 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants" +xref: Reactome:R-HSA-2900765 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants" +xref: Reactome:R-HSA-3000335 "SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA" +xref: Reactome:R-HSA-3134804 "STING ubiquitination by TRIM32 or TRIM56" +xref: Reactome:R-HSA-3134946 "DDX41 ubiquitination by TRIM21" +xref: Reactome:R-HSA-3249386 "DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1" +xref: Reactome:R-HSA-3780995 "NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2" +xref: Reactome:R-HSA-3781009 "NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1" +xref: Reactome:R-HSA-3788724 "Cdh1:APC/C ubiquitinates EHMT1 and EHMT2" +xref: Reactome:R-HSA-3797226 "Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease)" +xref: Reactome:R-HSA-400267 "BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins" +xref: Reactome:R-HSA-4332236 "CBL neddylates TGFBR2" +xref: Reactome:R-HSA-446877 "TRAF6 is K63 poly-ubiquitinated" +xref: Reactome:R-HSA-450358 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation" +xref: Reactome:R-HSA-451418 "Pellino ubiquitinates IRAK1" +xref: Reactome:R-HSA-5205682 "Parkin promotes the ubiquitination of mitochondrial substrates" +xref: Reactome:R-HSA-5357757 "BIRC(cIAP1/2) ubiquitinates RIPK1" +xref: Reactome:R-HSA-5362412 "SYVN1 ubiquitinates Hh C-terminal fragments" +xref: Reactome:R-HSA-5483238 "Hh processing variants are ubiquitinated" +xref: Reactome:R-HSA-5607725 "SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP" +xref: Reactome:R-HSA-5607728 "beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex" +xref: Reactome:R-HSA-5607756 "TRAF6 oligomer autoubiquitinates" +xref: Reactome:R-HSA-5607757 "K63polyUb-TRAF6 ubiquitinates TAK1" +xref: Reactome:R-HSA-5610742 "SCF(beta-TrCP) ubiquitinates p-GLI1" +xref: Reactome:R-HSA-5610745 "SCF(beta-TrCP) ubiquitinates p-GLI2" +xref: Reactome:R-HSA-5610746 "SCF(beta-TrCP) ubiquitinates p-GLI3" +xref: Reactome:R-HSA-5652009 "RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA" +xref: Reactome:R-HSA-5655170 "RCHY1 monoubiquitinates POLH" +xref: Reactome:R-HSA-5660753 "SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA" +xref: Reactome:R-HSA-5667107 "SIAH1, SIAH2 ubiquitinate SNCAIP" +xref: Reactome:R-HSA-5667111 "PARK2 K63-Ubiquitinates SNCAIP" +xref: Reactome:R-HSA-5668454 "K63polyUb-cIAP1,2 ubiquitinates TRAF3" +xref: Reactome:R-HSA-5668534 "cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK" +xref: Reactome:R-HSA-5675470 "BIRC2/3 (cIAP1/2) is autoubiquitinated" +xref: Reactome:R-HSA-5684250 "SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2" +xref: Reactome:R-HSA-5691108 "SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2" +xref: Reactome:R-HSA-5693108 "TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains" +xref: Reactome:R-HSA-69598 "Ubiquitination of phosphorylated Cdc25A" +xref: Reactome:R-HSA-741386 "RIP2 induces K63-linked ubiquitination of NEMO" +xref: Reactome:R-HSA-75824 "Ubiquitination of Cyclin D1" +xref: Reactome:R-HSA-870449 "TRIM33 monoubiquitinates SMAD4" +xref: Reactome:R-HSA-8948709 "DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3" +xref: Reactome:R-HSA-8956106 "VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha" +xref: Reactome:R-HSA-9013069 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH3" +xref: Reactome:R-HSA-9013974 "Auto-ubiquitination of TRAF3 within activated TLR3 complex" +xref: Reactome:R-HSA-9014342 "K63-linked ubiquitination of RIP1 bound to the activated TLR complex" +xref: Reactome:R-HSA-918224 "DDX58 is K63 polyubiquitinated" +xref: Reactome:R-HSA-936412 "RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS" +xref: Reactome:R-HSA-936942 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2" +xref: Reactome:R-HSA-936986 "Activated TRAF6 synthesizes unanchored polyubiquitin chains" +xref: Reactome:R-HSA-9628444 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation" +xref: Reactome:R-HSA-9645394 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation" +xref: Reactome:R-HSA-9645414 "Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer" +xref: Reactome:R-HSA-9688831 "STUB1 ubiquitinates RIPK3 at K55, K363" +xref: Reactome:R-HSA-9701000 "BRCA1:BARD1 heterodimer autoubiquitinates" +xref: Reactome:R-HSA-975118 "TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex" +xref: Reactome:R-HSA-975147 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane" +xref: Reactome:R-HSA-983140 "Transfer of Ub from E2 to substrate and release of E2" +xref: Reactome:R-HSA-983153 "E1 mediated ubiquitin activation" +xref: Reactome:R-HSA-983156 "Polyubiquitination of substrate" +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0005634 +name: nucleus +def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] +synonym: "cell nucleus" EXACT [] +synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757] +xref: NIF_Subcellular:sao1702920020 +xref: Wikipedia:Cell_nucleus + +[Term] +id: GO:0008150 +name: biological_process +def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +created_by: jl +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0016301 +name: kinase activity +def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] +comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. +synonym: "phosphokinase activity" EXACT [] +xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm" +xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines" +is_a: GO:0003674 ! molecular_function + +[Term] +id: GO:0019107 +name: myristoyltransferase activity +def: "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule." [GOC:ai] +xref: Reactome:R-HSA-141367 "Myristoylation of tBID by NMT1" +xref: Reactome:R-HSA-162914 "Myristoylation of Nef" +is_a: GO:0003674 ! molecular_function + +[Term] +id: OGMS:0000031 +name: disease +def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [] +is_a: BFO:0000016 ! disposition + +[Term] +id: PATO:0000001 +name: quality +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] +is_a: BFO:0000020 ! specifically dependent continuant + +[Term] +id: PATO:0000402 +name: branched +def: "A branchiness quality inhering in a bearer by virtue of the bearer's having branches." [WordNet:WordNet] +synonym: "ramified" EXACT [] +synonym: "ramiform" EXACT [] +is_a: PATO:0000001 ! quality +property_value: RO:0002604 PATO:0000414 + +[Term] +id: PATO:0001199 +name: linear +def: "A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel." [ISBN:0881923214] +is_a: PATO:0000001 ! quality + +[Term] +id: PATO:0002124 +name: laminar +def: "A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer." [PATOC:GVG] +is_a: PATO:0000001 ! quality +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +creation_date: 2009-10-06T04:37:14Z + +[Term] +id: RO:0002310 +name: exposure event or process +def: "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." [] +is_a: BFO:0000015 ! process +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string +property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI +property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/173" xsd:anyURI +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-06-05T17:55:39Z + +[Term] +id: RO:0002532 +name: sequentially ordered entity +def: "Any entity that is ordered in discrete units along a linear axis." [] +relationship: RO:0002524 RO:0002533 ! has subsequence sequence atomic unit +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 + +[Term] +id: RO:0002533 +name: sequence atomic unit +def: "Any individual unit of a collection of like units arranged in a linear order" [] +is_a: RO:0002532 ! sequentially ordered entity +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." xsd:string + +[Term] +id: RO:0002534 +name: sequence bearer +def: "Any entity that can be divided into parts such that each part is an atomical unit of a sequence" [] +is_a: RO:0002532 ! sequentially ordered entity +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." xsd:string + +[Term] +id: RO:0002577 +name: system +def: "A material entity consisting of multiple components that are causally integrated." [] +is_a: BFO:0000040 ! material entity +property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.jbiomedsem.com/content/4/1/43" xsd:string + +[Term] +id: UPHENO:0001001 +name: phenotype +is_a: PATO:0000001 ! quality + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: RO:0040042 BFO:0000004 +property_value: RO:0040042 BFO:0000017 +property_value: RO:0040042 BFO:0000019 +property_value: RO:0040042 BFO:0000020 +property_value: RO:0040042 BFO:0000031 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: BFO:0000054 +name: realized in +comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realized in" xsd:string +property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string +property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string +property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string +property_value: IAO:0000118 "is realized by" xsd:string +property_value: IAO:0000118 "realized_in" xsd:string +property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +inverse_of: BFO:0000055 ! realizes + +[Typedef] +id: BFO:0000055 +name: realizes +comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process +property_value: IAO:0000111 "realizes" xsd:string +property_value: IAO:0000112 "this disease course realizes this disease" xsd:string +property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string +property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string +property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl +domain: BFO:0000015 ! process +range: BFO:0000017 ! realizable entity + +[Typedef] +id: BFO:0000060 +name: obsolete preceded by +comment: accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062 +is_transitive: true +is_obsolete: true + +[Typedef] +id: BFO:0000062 +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: BFO:0000050 BFO:0000062 +holds_over_chain: RO:0002091 BFO:0000062 +holds_over_chain: RO:0002092 BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + +[Typedef] +id: BFO:0000063 +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: BFO:0000050 BFO:0000063 +holds_over_chain: RO:0002092 BFO:0000063 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000050 BFO:0000066 +inverse_of: BFO:0000067 ! contains process +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Typedef] +id: ENVO:01003004 +name: derives from part of +def: "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." [] + +[Typedef] +id: RO:0000052 +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: RO:0002314 ! characteristic of part of +inverse_of: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000053 +name: has characteristic +def: "Inverse of characteristic_of" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant +is_inverse_functional: true + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: BFO:0000051 RO:0000057 + +[Typedef] +id: RO:0000058 +name: is concretized as +def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000020 ! specifically dependent continuant +inverse_of: RO:0000059 ! concretizes + +[Typedef] +id: RO:0000059 +name: concretizes +def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] +property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string +property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: RO:0000079 +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 ! function +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000085 ! has function + +[Typedef] +id: RO:0000080 +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000086 ! has quality + +[Typedef] +id: RO:0000081 +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: RO:0000052 ! characteristic of +inverse_of: RO:0000087 ! has role + +[Typedef] +id: RO:0000085 +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000034 ! function +is_a: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 ! quality +is_a: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000087 +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000023 ! role +is_a: RO:0000053 ! has characteristic + +[Typedef] +id: RO:0000091 +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000016 ! disposition +is_a: RO:0000053 ! has characteristic +inverse_of: RO:0000092 ! disposition of + +[Typedef] +id: RO:0000092 +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +is_a: RO:0000052 ! characteristic of + +[Typedef] +id: RO:0000300 +name: obsolete in neural circuit with +def: "OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons." [] +comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_obsolete: true + +[Typedef] +id: RO:0000301 +name: obsolete upstream in neural circuit with +def: "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first." [] +comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_obsolete: true + +[Typedef] +id: RO:0000302 +name: obsolete downstream in neural circuit with +def: "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first." [] +comment: Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_obsolete: true + +[Typedef] +id: RO:0001000 +name: derives from +def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +subset: ro-eco +property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string +property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string +property_value: IAO:0000118 "derives_from" xsd:string +property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +inverse_of: RO:0001001 ! derives into + +[Typedef] +id: RO:0001001 +name: derives into +def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] +subset: ro-eco +property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string +property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string +property_value: IAO:0000118 "derives_into" xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000111 "is location of" xsd:string +property_value: IAO:0000112 "my head is the location of my brain" xsd:string +property_value: IAO:0000112 "this cage is the location of this rat" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000118 "location_of" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001018 +name: contained in +subset: ro-eco +property_value: IAO:0000111 "contained in" xsd:string +property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string +property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string +property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string +property_value: IAO:0000118 "contained_in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0001025 BFO:0000050 +inverse_of: RO:0001019 ! contains + +[Typedef] +id: RO:0001019 +name: contains +subset: ro-eco +property_value: IAO:0000111 "contains" xsd:string +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0001020 +name: is allergic trigger for +def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] +property_value: IAO:0000112 "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" xsd:string +domain: BFO:0000040 ! material entity +is_a: RO:0003302 ! causes or contributes to condition +inverse_of: RO:0001022 ! has allergic trigger + +[Typedef] +id: RO:0001021 +name: is autoimmune trigger for +def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] +domain: BFO:0000040 ! material entity +is_a: RO:0003302 ! causes or contributes to condition +inverse_of: RO:0001023 ! has autoimmune trigger + +[Typedef] +id: RO:0001022 +name: has allergic trigger +def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] +property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" xsd:string +range: BFO:0000040 ! material entity +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0001023 +name: has autoimmune trigger +def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] +range: BFO:0000040 ! material entity +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string +property_value: IAO:0000111 "located in" xsd:string +property_value: IAO:0000112 "my brain is located in my head" xsd:string +property_value: IAO:0000112 "this rat is located in this cage" xsd:string +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000118 "located_in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002000 +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string +property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: RO:0002323 ! mereotopologically related to +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002001 +name: aligned with +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_transitive: true + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002003 +name: electrically_synapsed_to +def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002004 +name: tracheates +def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure +is_a: RO:0001018 ! contained in + +[Typedef] +id: RO:0002005 +name: innervated_by +property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0001001 ! neuron projection bundle +inverse_of: RO:0002134 ! innervates + +[Typedef] +id: RO:0002006 +name: has synaptic terminal of +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_a: RO:0002131 ! overlaps +inverse_of: RO:0002130 ! has synaptic terminal in + +[Typedef] +id: RO:0002007 +name: bounding layer of +def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] +comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +range: BFO:0000040 ! material entity +is_a: BFO:0000050 ! part of + +[Typedef] +id: RO:0002008 +name: coincident with +def: "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." [] +comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. +subset: ro-eco +property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002009 +name: cell expresses +def: "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." [] +property_value: http://purl.org/dc/terms/description "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +domain: CL:0000000 ! cell +is_a: RO:0002292 ! expresses + +[Typedef] +id: RO:0002010 +name: regulates in other organism +def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002011 +name: regulates transport of +def: "A relationship that holds between a process that regulates a transport process and the entity transported by that process." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +holds_over_chain: RO:0002211 RO:0002313 + +[Typedef] +id: RO:0002012 +name: occurrent part of +def: "A part of relation that applies only between occurrents." [] +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: BFO:0000050 ! part of +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002016 +name: has necessary component activity +comment: A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. +is_a: RO:0002017 ! has component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:36:08Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002019 +name: has ligand +def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] +is_a: RO:0002233 ! has input +created_by: dos +creation_date: 2017-07-19T17:30:36Z + +[Typedef] +id: RO:0002020 +name: transports +def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] +is_a: RO:0002313 ! transports or maintains localization of +created_by: dos +creation_date: 2017-07-20T17:11:08Z + +[Typedef] +id: RO:0002021 +name: occurs across +def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] +is_a: RO:0002479 ! has part that occurs in +created_by: dos +creation_date: 2017-07-20T17:19:37Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +is_a: RO:0002334 ! regulated by +inverse_of: RO:0002578 ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002630 ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002629 ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +is_functional: true +is_a: RO:0002017 ! has component activity +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002026 +name: in register with +def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] +domain: http://xmlns.com/foaf/0.1/image +range: http://xmlns.com/foaf/0.1/image +is_a: RO:0002323 ! mereotopologically related to +created_by: dos +creation_date: 2017-12-07T12:58:06Z + +[Typedef] +id: RO:0002081 +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002082 +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + +[Typedef] +id: RO:0002083 +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + +[Typedef] +id: RO:0002084 +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: RO:0002222 ! temporally related to +inverse_of: RO:0002093 ! ends during + +[Typedef] +id: RO:0002085 +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: RO:0002088 ! during which starts +inverse_of: RO:0002092 ! happens during + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +holds_over_chain: RO:0002093 BFO:0000062 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +holds_over_chain: RO:0002224 RO:0002230 +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + +[Typedef] +id: RO:0002088 +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: RO:0002222 ! temporally related to +inverse_of: RO:0002091 ! starts during + +[Typedef] +id: RO:0002089 +name: starts before +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +holds_over_chain: RO:0002091 BFO:0000060 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: RO:0002575 BFO:0000063 +holds_over_chain: RO:0002230 RO:0002224 +is_a: BFO:0000063 ! precedes + +[Typedef] +id: RO:0002091 +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002092 +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: RO:0002091 ! starts during +is_a: RO:0002093 ! ends during + +[Typedef] +id: RO:0002093 +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002100 +name: has soma location +def: "Relation between a neuron and an anatomical structure that its soma is part of." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +domain: CL:0000540 ! neuron +range: CARO:0000003 ! connected anatomical structure +is_a: RO:0002131 ! overlaps +transitive_over: BFO:0000050 ! part of +expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002101 +name: fasciculates with +def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "fasciculates with" xsd:string +property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string +property_value: RO:0001900 RO:0001901 +domain: CL:0000540 ! neuron +range: CARO:0001001 ! neuron projection bundle +is_a: RO:0002131 ! overlaps +inverse_of: RO:0002132 ! has fasciculating neuron projection + +[Typedef] +id: RO:0002102 +name: axon synapses in +def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +domain: CL:0000540 ! neuron +is_a: RO:0002113 ! has presynaptic terminal in +transitive_over: BFO:0000050 ! part of +expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] + +[Typedef] +id: RO:0002103 +name: synapsed by +def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002485 ! receives input from +inverse_of: RO:0002120 ! synapsed to +expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002104 +name: has plasma membrane part +def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] +property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 +property_value: RO:0001900 RO:0001901 +domain: CARO:0000006 ! material anatomical entity +range: CARO:0000006 ! material anatomical entity +is_a: BFO:0000051 ! has part +expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] + +[Typedef] +id: RO:0002105 +name: synapsed_via_type_Ib_bouton_to +def: "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton." [] +comment: Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002120 ! synapsed to +inverse_of: RO:0002109 ! synapsed_by_via_type_Ib_bouton +expand_expression_to: "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" [] + +[Typedef] +id: RO:0002106 +name: synapsed_via_type_Is_bouton_to +def: "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." [] +comment: Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002120 ! synapsed to +inverse_of: RO:0002112 ! synapsed_by_via_type_Is_bouton +expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" [] + +[Typedef] +id: RO:0002107 +name: synapsed_via_type_II_bouton_to +def: "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." [] +comment: Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002120 ! synapsed to +inverse_of: RO:0002108 ! synapsed_by_via_type_II_bouton +expand_expression_to: "BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" [] + +[Typedef] +id: RO:0002108 +name: synapsed_by_via_type_II_bouton +def: "Relation between a muscle and a motor neuron that synapses to it via a type II bouton." [] +comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002103 ! synapsed by +expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" [] + +[Typedef] +id: RO:0002109 +name: synapsed_by_via_type_Ib_bouton +def: "Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton." [] +comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002103 ! synapsed by +expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] + +[Typedef] +id: RO:0002110 +name: has postsynaptic terminal in +def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "synapsed in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: CL:0000540 ! neuron +is_a: RO:0002130 ! has synaptic terminal in +inverse_of: RO:0002113 ! has presynaptic terminal in +transitive_over: BFO:0000050 ! part of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] + +[Typedef] +id: RO:0002111 +name: releases neurotransmitter +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "has neurotransmitter" xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: BFO:0000040 ! material entity + +[Typedef] +id: RO:0002112 +name: synapsed_by_via_type_Is_bouton +def: "Relation between a muscle and a motor neuron that synapses to it via a type Is bouton." [] +comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-5948-3092 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002103 ! synapsed by +expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] + +[Typedef] +id: RO:0002113 +name: has presynaptic terminal in +def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "synapses in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: CL:0000540 ! neuron +is_a: RO:0002130 ! has synaptic terminal in +transitive_over: BFO:0000050 ! part of +expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] + +[Typedef] +id: RO:0002114 +name: synapsed_via_type_III_bouton_to +def: "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." [] +comment: Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002120 ! synapsed to +inverse_of: RO:0002115 ! synapsed_by_via_type_III_bouton +expand_expression_to: "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" [] + +[Typedef] +id: RO:0002115 +name: synapsed_by_via_type_III_bouton +def: "Relation between a muscle and a motor neuron that synapses to it via a type III bouton.\n" [] +comment: Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002103 ! synapsed by +expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" [] + +[Typedef] +id: RO:0002120 +name: synapsed to +def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] +comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002486 ! sends output to +expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002121 +name: dendrite synapsed in +def: "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n " [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +domain: CL:0000540 ! neuron +is_a: RO:0002110 ! has postsynaptic terminal in +transitive_over: BFO:0000050 ! part of +expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] + +[Typedef] +id: RO:0002130 +name: has synaptic terminal in +def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has synapse in" xsd:string +property_value: RO:0001900 RO:0001901 +domain: CL:0000540 ! neuron +is_a: RO:0002131 ! overlaps +transitive_over: BFO:0000050 ! part of +expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: RO:0001900 RO:0001901 +holds_over_chain: BFO:0000050 BFO:0000050 +holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 RO:0002131 +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to +transitive_over: BFO:0000050 ! part of +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002132 +name: has fasciculating neuron projection +def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has fasciculating component" xsd:string +property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string +property_value: RO:0001900 RO:0001901 +domain: CARO:0001001 ! neuron projection bundle +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0002134 +name: innervates +def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: RO:0001900 RO:0001901 +domain: CARO:0001001 ! neuron projection bundle +transitive_over: BFO:0000050 ! part of +expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002150 +name: continuous with +def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "connected to" xsd:string +property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso "FMA:85972" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002151 +name: partially overlaps +def: "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" xsd:string +property_value: IAO:0000118 "proper overlaps" xsd:string +property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (proper_overlaps ?x ?y)\n (and \n (overlaps ?x ?y)\n (not (part_of ?x ?y)) \n (not (part_of ?y ?x)))))" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0002156 +name: derived by descent from +def: "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "ancestral_stucture_of" xsd:string +property_value: IAO:0000118 "evolutionarily_descended_from" xsd:string +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to +inverse_of: RO:0002157 ! has derived by descendant + +[Typedef] +id: RO:0002157 +name: has derived by descendant +def: "inverse of derived by descent from" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002158 +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string +holds_over_chain: RO:0002156 RO:0002157 +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002159 +name: serially homologous to +property_value: IAO:0000114 IAO:0000125 +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +range: CARO:0001010 ! organism or virus or viroid +holds_over_chain: BFO:0000050 RO:0002162 +holds_over_chain: BFO:0000051 RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002206 RO:0002162 +holds_over_chain: RO:0002214 RO:0002162 +holds_over_chain: RO:0002215 RO:0002162 +holds_over_chain: RO:0002225 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +holds_over_chain: RO:0002295 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002163 +name: spatially disjoint from +def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 +property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to +expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002170 +name: connected to +def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] +property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002176 +name: connects +def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] +property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string +property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +domain: BFO:0000004 ! independent continuant +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002177 +name: attached to part of +def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure +holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002323 ! mereotopologically related to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002178 +name: supplies +def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002179 +name: drains +def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002180 +name: has component +def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002200 +name: has phenotype +def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +range: UPHENO:0001001 ! phenotype +is_a: RO:0016001 ! has phenotype or disease +inverse_of: RO:0002201 ! phenotype of + +[Typedef] +id: RO:0002201 +name: phenotype of +def: "inverse of has phenotype" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_functional: true + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + +[Typedef] +id: RO:0002204 +name: gene product of +def: "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: BFO:0000004 ! independent continuant +range: BFO:0000002 ! continuant +holds_over_chain: RO:0002512 RO:0002510 +is_a: RO:0002330 ! genomically related to +inverse_of: RO:0002205 ! has gene product + +[Typedef] +id: RO:0002205 +name: has gene product +def: "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" [] +property_value: IAO:0000112 "every HOTAIR lncRNA is the gene product of some HOXC gene" xsd:string +property_value: IAO:0000112 "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: BFO:0000002 ! continuant +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0002511 RO:0002513 +is_a: RO:0002330 ! genomically related to + +[Typedef] +id: RO:0002206 +name: expressed in +def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] +property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: BFO:0000002 ! continuant +range: CARO:0000006 ! material anatomical entity +is_a: RO:0002330 ! genomically related to +inverse_of: RO:0002292 ! expresses +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002207 +name: directly develops from +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000119 "FBbt" xsd:string +property_value: RO:0002575 RO:0002202 +is_a: RO:0002202 ! develops from +inverse_of: RO:0002210 ! directly develops into + +[Typedef] +id: RO:0002208 +name: parasitoid of +def: "A parasite that kills or sterilizes its host" [] +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002209 ! has parasitoid + +[Typedef] +id: RO:0002209 +name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002210 +name: directly develops into +def: "inverse of directly develops from" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "developmental precursor of" xsd:string +is_a: RO:0002203 ! develops into + +[Typedef] +id: RO:0002211 +name: regulates +def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "GO" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string +property_value: IAO:0000589 "regulates (processual)" xsd:string +property_value: IAO:0000600 "false" xsd:boolean +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: RO:0002230 RO:0002211 +holds_over_chain: RO:0002578 RO:0002578 +is_transitive: true +is_a: RO:0002411 ! causally upstream of +inverse_of: RO:0002334 ! regulated by +transitive_over: RO:0002025 ! has effector activity + +[Typedef] +id: RO:0002212 +name: negatively regulates +def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +property_value: RO:0004050 RO:0002211 +holds_over_chain: RO:0002230 RO:0002212 +is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect +inverse_of: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002213 +name: positively regulates +def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +property_value: RO:0004049 RO:0002211 +holds_over_chain: RO:0002212 RO:0002212 +holds_over_chain: RO:0002230 RO:0002213 +is_transitive: true +is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect +inverse_of: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002214 +name: has prototype +def: "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." [] +property_value: IAO:0000112 "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" xsd:string +property_value: IAO:0000112 "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" xsd:string +property_value: IAO:0000116 "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." xsd:string +property_value: IAO:0000116 "TODO: add homeomorphy axiom" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 + +[Typedef] +id: RO:0002215 +name: capable of +def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has function in" xsd:string +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002217 +name: obsolete actively participates in +def: "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" [] +comment: Obsoleted as the inverse property was obsoleted. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "agent in" xsd:string +is_obsolete: true +replaced_by: RO:0002608 + +[Typedef] +id: RO:0002218 +name: obsolete has active participant +def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has agent" xsd:string +is_obsolete: true +replaced_by: RO:0002500 + +[Typedef] +id: RO:0002219 +name: surrounded by +def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002220 ! adjacent to +inverse_of: RO:0002221 ! surrounds + +[Typedef] +id: RO:0002220 +name: adjacent to +def: "x adjacent to y if and only if x and y share a boundary." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"} +property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string +property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string +property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0001900 RO:0001901 +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_a: RO:0002163 ! spatially disjoint from + +[Typedef] +id: RO:0002221 +name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0001900 RO:0001901 +is_a: RO:0002220 ! adjacent to + +[Typedef] +id: RO:0002222 +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. +subset: ro-eco +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "Allen" xsd:string +is_a: BFO:0000050 ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: RO:0002224 ! starts with + +[Typedef] +id: RO:0002224 +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: BFO:0000051 ! has part +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002225 +name: develops from part of +def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002207 BFO:0000050 +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002226 +name: develops in +def: "x develops_in y if x is located in y whilst x is developing" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "EHDAA2" xsd:string +property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string +domain: CARO:0000000 ! anatomical entity +holds_over_chain: RO:0002207 RO:0001025 +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002227 +name: obligate parasite of +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002228 +name: facultative parasite of +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: BFO:0000050 ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: RO:0002230 ! ends with + +[Typedef] +id: RO:0002230 +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: BFO:0000051 ! has part +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002231 +name: has start location +def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "starts with process that occurs in" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0002224 BFO:0000066 +is_a: RO:0002479 ! has part that occurs in + +[Typedef] +id: RO:0002232 +name: has end location +def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "ends with process that occurs in" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0002230 BFO:0000066 +is_a: RO:0002479 ! has part that occurs in + +[Typedef] +id: RO:0002233 +name: has input +def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "consumes" xsd:string +domain: BFO:0000015 ! process +holds_over_chain: RO:0002224 RO:0002233 +is_a: RO:0000057 ! has participant +inverse_of: RO:0002352 ! input of + +[Typedef] +id: RO:0002234 +name: has output +def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "produces" xsd:string +holds_over_chain: RO:0002230 RO:0002234 +is_a: RO:0000057 ! has participant +inverse_of: RO:0002353 ! output of + +[Typedef] +id: RO:0002235 +name: stem parasite of +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002236 +name: root parasite of +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002237 +name: hemiparasite of +def: "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002238 +name: has component participant +def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string +is_a: RO:0000057 ! has participant + +[Typedef] +id: RO:0002240 +name: has exposure receptor +def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] +property_value: IAO:0000119 "ExO:0000001" xsd:string +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002241 +name: has exposure stressor +def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] +property_value: IAO:0000119 "ExO:0000000" xsd:string +is_a: RO:0002309 ! has exposure stimulus + +[Typedef] +id: RO:0002242 +name: has exposure route +def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] +property_value: IAO:0000119 "ExO:0000055" xsd:string +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002243 +name: has exposure transport path +def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI +is_a: RO:0002244 ! related via exposure to + +[Typedef] +id: RO:0002244 +name: related via exposure to +def: "Any relationship between an exposure event or process and any other entity." [] +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." xsd:string +domain: RO:0002310 ! exposure event or process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002245 +name: over-expressed in +def: "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." [] +is_a: RO:0002206 ! expressed in + +[Typedef] +id: RO:0002246 +name: under-expressed in +def: "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." [] +is_a: RO:0002206 ! expressed in + +[Typedef] +id: RO:0002248 +name: has active ingredient +def: "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." [] +synonym: "has active pharmaceutical ingredient" RELATED [] +synonym: "has active substance" EXACT [] +property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: BFO:0000051 ! has part +inverse_of: RO:0002249 ! active ingredient in + +[Typedef] +id: RO:0002249 +name: active ingredient in +def: "inverse of has active ingredient" [] +subset: RO:0002259 +is_a: BFO:0000050 ! part of + +[Typedef] +id: RO:0002252 +name: connecting branch of +def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] +property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string +property_value: RO:0004036 BFO:0000050 +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002253 ! has connecting branch + +[Typedef] +id: RO:0002253 +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +property_value: RO:0004036 BFO:0000051 +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity +holds_over_chain: BFO:0000051 RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + +[Typedef] +id: RO:0002255 +name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002203 BFO:0000050 +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002256 +name: developmentally induced by +def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "induced by" xsd:string +property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string +domain: CARO:0000006 ! material anatomical entity +range: CARO:0000006 ! material anatomical entity +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002257 ! developmentally induces + +[Typedef] +id: RO:0002257 +name: developmentally induces +def: "Inverse of developmentally induced by" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002386 ! has potential to developmentally induce + +[Typedef] +id: RO:0002258 +name: developmentally preceded by +def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] +comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "false" xsd:boolean +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002324 ! developmentally related to +inverse_of: RO:0002286 ! developmentally succeeded by + +[Typedef] +id: RO:0002260 +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +is_a: RO:0000087 ! has role + +[Typedef] +id: RO:0002261 +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +is_a: RO:0000087 ! has role + +[Typedef] +id: RO:0002262 +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +is_a: RO:0000087 ! has role + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 RO:0002411 +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 RO:0002418 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002285 +name: developmentally replaces +def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "replaces" xsd:string +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002286 +name: developmentally succeeded by +def: "Inverse of developmentally preceded by" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002287 +name: part of developmental precursor of +property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: BFO:0000050 RO:0002210 +is_a: RO:0002286 ! developmentally succeeded by + +[Typedef] +id: RO:0002291 +name: ubiquitously expressed in +def: "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002206 ! expressed in +inverse_of: RO:0002293 ! ubiquitously expresses + +[Typedef] +id: RO:0002292 +name: expresses +def: "Inverse of 'expressed in'" [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002330 ! genomically related to + +[Typedef] +id: RO:0002293 +name: ubiquitously expresses +def: "inverse of ubiquiotously expressed in" [] +subset: RO:0002259 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002292 ! expresses + +[Typedef] +id: RO:0002295 +name: results in developmental progression of +def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso Ontology:extensions +domain: GO:0008150 ! biological_process +range: CARO:0000000 ! anatomical entity +is_a: RO:0002324 ! developmentally related to + +[Typedef] +id: RO:0002296 +name: results in development of +def: "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI +is_a: RO:0002295 ! results in developmental progression of +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002297 +name: results in formation of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string +property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string +is_a: RO:0002234 ! has output +is_a: RO:0002295 ! results in developmental progression of +inverse_of: RO:0002354 ! formed as result of + +[Typedef] +id: RO:0002298 +name: results in morphogenesis of +def: "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string +property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string +is_a: RO:0002295 ! results in developmental progression of +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002299 +name: results in maturation of +def: "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string +property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string +is_a: RO:0002295 ! results in developmental progression of +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002300 +name: results in disappearance of +property_value: IAO:0000112 "foramen ovale closure SubClassOf results in disappearance of foramen ovale" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "May be merged into parent relation" xsd:string +is_a: RO:0002552 ! results in ending of + +[Typedef] +id: RO:0002301 +name: results in developmental regression of +property_value: IAO:0000112 "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "May be merged into parent relation" xsd:string +is_a: RO:0002552 ! results in ending of + +[Typedef] +id: RO:0002302 +name: is treated by substance +def: "Inverse of 'is substance that treats'" [] +subset: RO:0002259 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002410 ! causally related to +inverse_of: RO:0002606 ! is substance that treats + +[Typedef] +id: RO:0002303 +name: has habitat +def: "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." [] +comment: A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. +subset: ro-eco +property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 +property_value: IAO:0000118 "adapted for living in" xsd:string +domain: CARO:0001010 ! organism or virus or viroid +range: ENVO:01000254 ! environmental system +is_a: RO:0002321 ! ecologically related to + +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004049 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004050 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: RO:0002309 +name: has exposure stimulus +def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 +is_a: RO:0002244 ! related via exposure to +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-06-05T17:35:04Z + +[Typedef] +id: RO:0002312 +name: evolutionary variant of +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002313 +name: transports or maintains localization of +def: "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "regulates localization of" xsd:string +is_a: RO:0002337 ! related via localization to +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002314 +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002502 ! depends on +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002315 +name: results in acquisition of features of +def: "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string +range: CARO:0000003 ! connected anatomical structure +is_a: RO:0002295 ! results in developmental progression of +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002320 +name: evolutionarily related to +def: "A relationship that holds via some environmental process" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string + +[Typedef] +id: RO:0002321 +name: ecologically related to +def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] +subset: ro-eco +property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string + +[Typedef] +id: RO:0002322 +name: confers advantage in +subset: ro-eco +property_value: IAO:0000116 "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "adapted for" xsd:string +range: ENVO:01000254 ! environmental system +is_a: RO:0002321 ! ecologically related to + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0002324 +name: developmentally related to +def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string + +[Typedef] +id: RO:0002325 +name: colocalizes with +def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000112 "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002326 +name: contributes to +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." xsd:string +property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string +property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string +property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +is_a: RO:0002216 ! capable of part of +is_a: RO:0002329 ! part of structure that is capable of + +[Typedef] +id: RO:0002327 +name: enables +def: "c enables p iff c is capable of p and c acts to execute p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "catalyzes" xsd:string +property_value: IAO:0000118 "executes" xsd:string +property_value: IAO:0000118 "has" xsd:string +property_value: IAO:0000118 "is catalyzing" xsd:string +property_value: IAO:0000118 "is executing" xsd:string +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +is_a: RO:0002215 ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: BFO:0000051 ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "false" xsd:boolean +holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002330 +name: genomically related to +def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 BFO:0000050 +is_a: RO:0000056 ! participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002332 +name: regulates levels of +def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] +property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0000057 ! has participant +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002334 +name: regulated by +def: "inverse of regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000589 "regulated by (processual)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002335 +name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002336 +name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002337 +name: related via localization to +def: "A relationship that holds via some process of localization" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string +domain: BFO:0000015 ! process +range: BFO:0000002 ! continuant + +[Typedef] +id: RO:0002338 +name: has target start location +def: "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002344 ! results in transport to from or in +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002339 +name: has target end location +def: "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002344 ! results in transport to from or in +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002340 +name: imports +def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002020 ! transports + +[Typedef] +id: RO:0002341 +name: results in transport along +def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002337 ! related via localization to + +[Typedef] +id: RO:0002342 +name: results in transport across +def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002021 ! occurs across +is_a: RO:0002344 ! results in transport to from or in + +[Typedef] +id: RO:0002343 +name: results in growth of +property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002295 ! results in developmental progression of +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002344 +name: results in transport to from or in +property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002337 ! related via localization to + +[Typedef] +id: RO:0002345 +name: exports +def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002020 ! transports + +[Typedef] +id: RO:0002348 +name: results in commitment to +def: "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000112 "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +range: CL:0000000 ! cell +is_a: RO:0002295 ! results in developmental progression of + +[Typedef] +id: RO:0002349 +name: results in determination of +def: "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +range: CL:0000000 ! cell +is_a: RO:0002295 ! results in developmental progression of + +[Typedef] +id: RO:0002350 +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000050 ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002353 +name: output of +def: "inverse of has output" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002354 +name: formed as result of +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002353 ! output of + +[Typedef] +id: RO:0002355 +name: results in structural organization of +def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002295 ! results in developmental progression of +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002356 +name: results in specification of +def: "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +range: CL:0000000 ! cell +is_a: RO:0002295 ! results in developmental progression of + +[Typedef] +id: RO:0002357 +name: results in developmental induction of +def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002295 ! results in developmental progression of + +[Typedef] +id: RO:0002360 +name: has dendrite location +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0002371 +name: attached to +def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string +is_symmetric: true +is_a: RO:0002170 ! connected to +is_a: RO:0002177 ! attached to part of + +[Typedef] +id: RO:0002372 +name: has muscle origin +def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string +property_value: seeAlso http://dbpedia.org/property/origin +domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! connected anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002373 +name: has muscle insertion +def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string +property_value: seeAlso http://dbpedia.org/property/insertion +domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! connected anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002374 +name: derived from ancestral fusion of +def: "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" [] +comment: A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. +synonym: "has fused element" BROAD [] +property_value: IAO:0000112 "false" xsd:boolean +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 +is_a: RO:0002156 ! derived by descent from + +[Typedef] +id: RO:0002375 +name: in branching relationship with +def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string +property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string +property_value: RO:0004036 BFO:0000050 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002376 +name: tributary of +def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] +subset: ro-eco +property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string +property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "drains into" xsd:string +property_value: IAO:0000118 "drains to" xsd:string +property_value: IAO:0000118 "tributary channel of" xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string +property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI +property_value: seeAlso http://dbpedia.org/ontology/drainsTo +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002377 +name: distributary of +def: "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" [] +comment: This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes +subset: ro-eco +property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "branch of" xsd:string +property_value: IAO:0000118 "distributary channel of" xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002378 +name: anabranch of +def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "anastomoses with" xsd:string +is_a: RO:0002377 ! distributary of +disjoint_from: RO:0002382 ! proper distributary of +disjoint_from: RO:0002383 ! proper tributary of + +[Typedef] +id: RO:0002379 +name: spatially coextensive with +def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] +property_value: IAO:0000112 "A lump of clay and a statue" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0002380 +name: branching part of +def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] +subset: ro-eco +property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "FMA:85994" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +holds_over_chain: RO:0002377 RO:0002381 +is_a: BFO:0000050 ! part of +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002569 ! has branching part + +[Typedef] +id: RO:0002381 +name: main stem of +def: "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." [] +subset: ro-eco +property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: BFO:0000050 ! part of +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002382 +name: proper distributary of +def: "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002377 ! distributary of + +[Typedef] +id: RO:0002383 +name: proper tributary of +def: "x proper_tributary_of y iff x tributary_of y and x does not originate from y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002376 ! tributary of + +[Typedef] +id: RO:0002384 +name: has developmental potential involving +def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: CARO:0000000 ! anatomical entity +range: CARO:0000000 ! anatomical entity +is_a: RO:0002324 ! developmentally related to + +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002386 +name: has potential to developmentally induce +def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002388 +name: has potential to directly develop into +def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002387 ! has potential to develop into + +[Typedef] +id: RO:0002400 +name: has direct input +def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +property_value: IAO:0000112 "'protein catabolic process' SubClassOf has_direct_input some protein" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "directly consumes" xsd:string +property_value: IAO:0000232 "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" xsd:string +holds_over_chain: RO:0002224 RO:0002400 +is_a: RO:0002233 ! has input + +[Typedef] +id: RO:0002401 +name: obsolete has indirect input +comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_obsolete: true + +[Typedef] +id: RO:0002402 +name: obsolete has direct output +def: "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " [] +property_value: IAO:0000112 "translation SubClassOf has_direct_output some protein" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "directly produces" xsd:string +is_obsolete: true + +[Typedef] +id: RO:0002403 +name: obsolete has indirect output +comment: Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002411 RO:0002402 +is_obsolete: true + +[Typedef] +id: RO:0002404 +name: causally downstream of +def: "inverse of upstream of" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: BFO:0000062 ! preceded by +is_a: RO:0002427 ! causally downstream of or within +inverse_of: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002405 +name: immediately causally downstream of +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002087 ! immediately preceded by +is_a: RO:0002404 ! causally downstream of +inverse_of: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002406 +name: obsolete directly activates +comment: This term was obsoleted because it has the same meaning as 'directly positively regulates'. +is_obsolete: true +replaced_by: RO:0002629 + +[Typedef] +id: RO:0002407 +name: indirectly positively regulates +def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "indirectly activates" xsd:string +property_value: RO:0002579 RO:0002213 +holds_over_chain: RO:0002409 RO:0002409 +holds_over_chain: RO:0002629 RO:0002407 +holds_over_chain: RO:0002629 RO:0002629 +is_transitive: true +is_a: RO:0002213 ! positively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002629 ! directly positively regulates + +[Typedef] +id: RO:0002408 +name: obsolete directly inhibits +comment: This term was obsoleted because it has the same meaning as 'directly negatively regulates'. +is_obsolete: true +replaced_by: RO:0002630 + +[Typedef] +id: RO:0002409 +name: indirectly negatively regulates +def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "indirectly inhibits" xsd:string +property_value: RO:0002579 RO:0002212 +holds_over_chain: RO:0002630 RO:0002409 +holds_over_chain: RO:0002630 RO:0002630 +is_transitive: true +is_a: RO:0002212 ! negatively regulates +is_a: RO:0012012 ! indirectly regulates +transitive_over: RO:0002630 ! directly negatively regulates + +[Typedef] +id: RO:0002410 +name: causally related to +def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string + +[Typedef] +id: RO:0002411 +name: causally upstream of +def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_transitive: true +is_a: BFO:0000063 ! precedes +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002412 +name: immediately causally upstream of +def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0002575 RO:0002411 +is_a: RO:0002090 ! immediately precedes +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002413 +name: provides input for +def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] +property_value: IAO:0000116 "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "directly provides input for" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly provides input for (process to process)" xsd:string +holds_over_chain: RO:0002402 RO:0002400 +is_a: RO:0002412 ! immediately causally upstream of +is_a: RO:0002414 ! transitively provides input for + +[Typedef] +id: RO:0002414 +name: transitively provides input for +def: "transitive form of directly_provides_input_for" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." xsd:string +property_value: IAO:0000589 "transitively provides input for (process to process)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002418 +name: causally upstream of or within +def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] +synonym: "affects" RELATED [] +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "influences (processual)" xsd:string +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002424 +name: differs in +comment: This is an exploratory relation +property_value: IAO:0000116 "false" xsd:boolean +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" xsd:anyURI + +[Typedef] +id: RO:0002425 +name: differs in attribute of +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002424 ! differs in + +[Typedef] +id: RO:0002426 +name: differs in attribute +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +range: BFO:0000020 ! specifically dependent continuant +is_a: RO:0002424 ! differs in + +[Typedef] +id: RO:0002427 +name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002327 RO:0002211 +holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 RO:0002213 +holds_over_chain: RO:0002331 RO:0002213 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 RO:0002212 +holds_over_chain: RO:0002331 RO:0002212 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +name: involved in or involved in regulation of +def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002432 +name: is active in +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +synonym: "enables activity in" EXACT [] +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "executes activity in" xsd:string +holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002433 +name: contributes to morphology of +def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0002434 +name: interacts with +def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] +subset: ro-eco +synonym: "in pairwise interaction with" EXACT [] +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002435 +name: genetically interacts with +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI +property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso ECO:0000316 +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: seeAlso ECO:0000353 +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002437 +name: biotically interacts with +def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "interacts with on organism level" xsd:string +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true +is_a: RO:0002321 ! ecologically related to +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002438 +name: trophically interacts with +def: "An interaction relationship in which the partners are related via a feeding relationship." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002439 +name: preys on +def: "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" [] +subset: ro-eco +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string +property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000118 "is subject of predation interaction with" xsd:string +property_value: IAO:0000118 "preys upon" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string +is_a: RO:0002438 ! trophically interacts with +inverse_of: RO:0002458 ! preyed upon by + +[Typedef] +id: RO:0002440 +name: symbiotically interacts with +def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string +is_symmetric: true +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002441 +name: commensually interacts with +def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002442 +name: mutualistically interacts with +def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002443 +name: interacts with via parasite-host interaction +def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002444 +name: parasite of +subset: ro-eco +synonym: "direct parasite of" EXACT [] +property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "parasitizes" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string +is_a: RO:0002443 ! interacts with via parasite-host interaction +is_a: RO:0002454 ! has host +inverse_of: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002445 +name: parasitized by +subset: ro-eco +synonym: "directly parasitized by" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has parasite" xsd:string +property_value: IAO:0000118 "parasitised by" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string +is_a: RO:0002443 ! interacts with via parasite-host interaction +is_a: RO:0002453 ! host of + +[Typedef] +id: RO:0002446 +name: participates in a abiotic-biotic interaction with +def: "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." [] +subset: ro-eco +synonym: "semibiotically interacts with" RELATED [] +property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +is_a: RO:0002437 ! biotically interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: directly regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0011002 ! regulates activity of + +[Typedef] +id: RO:0002449 +name: directly negatively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000118 "directly inhibits" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002450 +name: directly positively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000118 "directly activates" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002451 +name: transmitted by +def: "A relationship that holds between a disease and organism" [] +property_value: IAO:0000112 "all dengue disease transmitted by some mosquito" xsd:string +property_value: IAO:0000116 "Add domain and range constraints" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002321 ! ecologically related to + +[Typedef] +id: RO:0002452 +name: has symptom +def: "A relation that holds between a disease or an organism and a phenotype" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: OGMS:0000031 ! disease +is_a: RO:0002200 ! has phenotype + +[Typedef] +id: RO:0002453 +name: host of +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002454 +name: has host +def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002455 +name: pollinates +subset: ro-eco +property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string +property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string +is_a: RO:0002442 ! mutualistically interacts with +inverse_of: RO:0002456 ! pollinated by + +[Typedef] +id: RO:0002456 +name: pollinated by +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has polinator" xsd:string +property_value: IAO:0000118 "is target of pollination interaction with" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string +is_a: RO:0002442 ! mutualistically interacts with + +[Typedef] +id: RO:0002457 +name: acquires nutrients from +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string +is_a: RO:0002438 ! trophically interacts with +inverse_of: RO:0002469 ! provides nutrients for + +[Typedef] +id: RO:0002458 +name: preyed upon by +def: "inverse of preys on" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has predator" xsd:string +property_value: IAO:0000118 "is target of predation interaction with" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002459 +name: is vector for +subset: ro-eco +property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string +is_a: RO:0002574 ! participates in a biotic-biotic interaction with +inverse_of: RO:0002460 ! has vector + +[Typedef] +id: RO:0002460 +name: has vector +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002461 +name: partner in +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string +is_a: RO:0000056 ! participates in + +[Typedef] +id: RO:0002462 +name: subject participant in +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string +is_a: RO:0002461 ! partner in + +[Typedef] +id: RO:0002463 +name: target participant in +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." xsd:string +is_a: RO:0002461 ! partner in + +[Typedef] +id: RO:0002464 +name: helper property (not for use in curation) +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002465 +name: is symbiosis +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002563 ! interaction relation helper property + +[Typedef] +id: RO:0002466 +name: is commensalism +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002465 ! is symbiosis + +[Typedef] +id: RO:0002467 +name: is mutualism +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002465 ! is symbiosis + +[Typedef] +id: RO:0002468 +name: is parasitism +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002465 ! is symbiosis + +[Typedef] +id: RO:0002469 +name: provides nutrients for +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002470 +name: eats +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "is subject of eating interaction with" xsd:string +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002471 +name: is eaten by +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "eaten by" xsd:string +property_value: IAO:0000118 "is target of eating interaction with" xsd:string +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002472 +name: is evidence for +def: "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002616 ! related via evidence or inference to +inverse_of: RO:0002558 ! has evidence + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002476 +name: child nucleus of +def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] +property_value: IAO:0000112 "ABal nucleus child nucleus of ABa nucleus (in C elegans)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." xsd:string +domain: GO:0005634 ! nucleus +range: GO:0005634 ! nucleus +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002477 +name: child nucleus of in hermaphrodite +def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002476 ! child nucleus of + +[Typedef] +id: RO:0002478 +name: child nucleus of in male +def: "A child nucleus relationship in which the cells are part of a male organism" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002476 ! child nucleus of + +[Typedef] +id: RO:0002479 +name: has part that occurs in +def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} + +[Typedef] +id: RO:0002480 +name: ubiquitinates +def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002481 +name: is kinase activity +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0002482 +name: is ubiquitination +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0002485 +name: receives input from +property_value: IAO:0000116 "See notes for inverse relation" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002170 ! connected to +inverse_of: RO:0002486 ! sends output to + +[Typedef] +id: RO:0002486 +name: sends output to +property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002487 +name: relation between physical entity and a process or stage +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002583 BFO:0000050 +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002488 ! existence starts during + +[Typedef] +id: RO:0002490 +name: existence overlaps +def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002487 ! relation between physical entity and a process or stage + +[Typedef] +id: RO:0002491 +name: existence starts and ends during +def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +synonym: "exists during" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002488 ! existence starts during +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002593 BFO:0000050 +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002494 +name: transformation of +def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_transitive: true +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002495 +name: immediate transformation of +def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0002575 RO:0002494 +is_a: RO:0002207 ! directly develops from +is_a: RO:0002494 ! transformation of + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: BFO:0000050 RO:0002496 +holds_over_chain: RO:0002258 RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: BFO:0000050 ! part of +transitive_over: BFO:0000062 ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: BFO:0000050 RO:0002497 +holds_over_chain: RO:0002286 RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: BFO:0000050 ! part of +transitive_over: BFO:0000063 ! precedes +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! process has causal agent + +[Typedef] +id: RO:0002501 +name: causal relation between processes +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002502 +name: depends on +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + +[Typedef] +id: RO:0002503 +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: RO:0002502 ! depends on + +[Typedef] +id: RO:0002505 +name: has intermediate +def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" [] +subset: ro-eco +property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has intermediate product" xsd:string +is_a: RO:0000057 ! has participant + +[Typedef] +id: RO:0002506 +name: causal relation between entities +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002507 +name: determined by +def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] +subset: ro-eco +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string +property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 +property_value: IAO:0000589 "determined by (system to material entity)" xsd:string +domain: RO:0002577 ! system +range: BFO:0000040 ! material entity +is_a: BFO:0000050 ! part of +is_a: RO:0002509 ! determined by part of +is_a: RO:0002559 ! causally influenced by +inverse_of: RO:0002508 ! determines + +[Typedef] +id: RO:0002508 +name: determines +def: "inverse of determined by" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000589 "determines (material entity to system)" xsd:string +is_a: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002509 +name: determined by part of +def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: RO:0002577 ! system +range: BFO:0000040 ! material entity +holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002506 ! causal relation between entities + +[Typedef] +id: RO:0002510 +name: transcribed from +def: "x is transcribed from y if and only if x is synthesized from template y" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_a: RO:0002330 ! genomically related to +inverse_of: RO:0002511 ! transcribed to + +[Typedef] +id: RO:0002511 +name: transcribed to +def: "inverse of transcribed from" [] +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_a: RO:0002330 ! genomically related to + +[Typedef] +id: RO:0002512 +name: ribosomal translation of +def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_a: RO:0002330 ! genomically related to +inverse_of: RO:0002513 ! ribosomally translates to + +[Typedef] +id: RO:0002513 +name: ribosomally translates to +def: "inverse of ribosomal translation of" [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_a: RO:0002330 ! genomically related to + +[Typedef] +id: RO:0002514 +name: sequentially related to +def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string +domain: RO:0002532 ! sequentially ordered entity +range: RO:0002532 ! sequentially ordered entity + +[Typedef] +id: RO:0002515 +name: sequentially adjacent to +def: "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcript" xsd:string +property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string +property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_a: RO:0002527 ! does not overlap sequence of + +[Typedef] +id: RO:0002516 +name: has start sequence +def: "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "started by" xsd:string +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_transitive: true +is_a: RO:0002524 ! has subsequence +inverse_of: RO:0002517 ! is start sequence of + +[Typedef] +id: RO:0002517 +name: is start sequence of +def: "inverse of has start sequence" [] +subset: RO:0002259 +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "starts" xsd:string +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_transitive: true +is_a: RO:0002525 ! is subsequence of + +[Typedef] +id: RO:0002518 +name: has end sequence +def: "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "ended by" xsd:string +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_transitive: true +is_a: RO:0002524 ! has subsequence +inverse_of: RO:0002519 ! is end sequence of + +[Typedef] +id: RO:0002519 +name: is end sequence of +def: "inverse of has end sequence" [] +subset: RO:0002259 +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "ends" xsd:string +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_transitive: true +is_a: RO:0002525 ! is subsequence of + +[Typedef] +id: RO:0002520 +name: is consecutive sequence of +def: "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_a: RO:0002524 ! has subsequence + +[Typedef] +id: RO:0002521 +name: is sequentially aligned with +def: "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000112 "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_symmetric: true +is_a: RO:0002514 ! sequentially related to + +[Typedef] +id: RO:0002522 +name: bounds sequence of +def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000112 "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_transitive: true +is_a: RO:0002514 ! sequentially related to +inverse_of: RO:0002523 ! is bound by sequence of + +[Typedef] +id: RO:0002523 +name: is bound by sequence of +def: "inverse of bounds sequence of" [] +subset: RO:0002259 +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_transitive: true +is_a: RO:0002514 ! sequentially related to + +[Typedef] +id: RO:0002524 +name: has subsequence +def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "contains" xsd:string +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI +is_transitive: true +is_a: BFO:0000051 ! has part +is_a: RO:0002522 ! bounds sequence of +is_a: RO:0002526 ! overlaps sequence of +inverse_of: RO:0002525 ! is subsequence of + +[Typedef] +id: RO:0002525 +name: is subsequence of +def: "inverse of has subsequence" [] +subset: RO:0002259 +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "contained by" xsd:string +is_transitive: true +is_a: BFO:0000050 ! part of +is_a: RO:0002523 ! is bound by sequence of +is_a: RO:0002526 ! overlaps sequence of + +[Typedef] +id: RO:0002526 +name: overlaps sequence of +def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002524 RO:0002525 +is_symmetric: true +is_a: RO:0002131 ! overlaps +is_a: RO:0002514 ! sequentially related to + +[Typedef] +id: RO:0002527 +name: does not overlap sequence of +def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "disconnected from" xsd:string +is_symmetric: true +is_a: RO:0002514 ! sequentially related to + +[Typedef] +id: RO:0002528 +name: is upstream of sequence of +def: "inverse of downstream of sequence of" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_transitive: true +is_a: RO:0002527 ! does not overlap sequence of + +[Typedef] +id: RO:0002529 +name: is downstream of sequence of +def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_transitive: true +is_a: RO:0002527 ! does not overlap sequence of +inverse_of: RO:0002529 ! is downstream of sequence of + +[Typedef] +id: RO:0002530 +name: is immediately downstream of sequence of +def: "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000112 "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: RO:0002575 RO:0002529 +is_a: RO:0002515 ! sequentially adjacent to +is_a: RO:0002529 ! is downstream of sequence of + +[Typedef] +id: RO:0002531 +name: is immediately upstream of sequence of +def: "inverse of immediately downstream of" [] +property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract +property_value: IAO:0000112 "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002515 ! sequentially adjacent to +is_a: RO:0002528 ! is upstream of sequence of + +[Typedef] +id: RO:0002551 +name: has skeleton +def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] +property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has supporting framework" xsd:string +property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +is_a: BFO:0000051 ! has part +inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true + +[Typedef] +id: RO:0002552 +name: results in ending of +def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002295 ! results in developmental progression of +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002553 +name: hyperparasite of +def: "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" [] +subset: ro-eco +synonym: "epiparasite of" RELATED [] +synonym: "hyperparasitoid of" NARROW [] +property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string +holds_over_chain: RO:0002444 RO:0002444 +is_a: RO:0002454 ! has host +inverse_of: RO:0002554 ! hyperparasitized by + +[Typedef] +id: RO:0002554 +name: hyperparasitized by +def: "inverse of hyperparasite of" [] +subset: ro-eco +subset: RO:0002259 +synonym: "has epiparasite" RELATED [] +synonym: "has hyperparasite" RELATED [] +synonym: "hyperparasitoidized by" RELATED [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002445 RO:0002445 +is_a: RO:0002453 ! host of + +[Typedef] +id: RO:0002555 +name: allelopath of +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string +property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002556 +name: pathogen of +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002454 ! has host +inverse_of: RO:0002557 ! has pathogen + +[Typedef] +id: RO:0002557 +name: has pathogen +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002453 ! host of + +[Typedef] +id: RO:0002558 +name: has evidence +def: "inverse of is evidence for" [] +comment: x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/25052702 +is_a: RO:0002616 ! related via evidence or inference to + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string +is_a: RO:0002506 ! causal relation between entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002563 +name: interaction relation helper property +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI +is_a: RO:0002464 ! helper property (not for use in curation) + +[Typedef] +id: RO:0002564 +name: molecular interaction relation helper property +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002563 ! interaction relation helper property + +[Typedef] +id: RO:0002565 +name: results in movement of +def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "" xsd:string +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002566 +name: causally influences +def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002506 ! causal relation between entities + +[Typedef] +id: RO:0002567 +name: biomechanically related to +def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002568 +name: has muscle antagonist +def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002569 +name: has branching part +def: "inverse of branching part of" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_transitive: true +is_a: BFO:0000051 ! has part +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002570 +name: conduit for +def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "UBERON:cjm" xsd:string +property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0002571 +name: lumen of +def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "GOC:cjm" xsd:string +range: BFO:0000040 ! material entity +is_a: BFO:0000050 ! part of + +[Typedef] +id: RO:0002572 +name: luminal space of +def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: BFO:0000141 ! immaterial entity +is_a: RO:0002571 ! lumen of + +[Typedef] +id: RO:0002573 +name: has modifier +def: "A relation that holds between an attribute or a qualifier and another attribute." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string +domain: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0002574 +name: participates in a biotic-biotic interaction with +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +domain: CARO:0001010 ! organism or virus or viroid +range: CARO:0001010 ! organism or virus or viroid +is_a: RO:0002437 ! biotically interacts with + +[Typedef] +id: RO:0002576 +name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: CARO:0000003 ! connected anatomical structure +range: CARO:0000003 ! connected anatomical structure +is_a: BFO:0000050 ! part of + +[Typedef] +id: RO:0002578 +name: directly regulates +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: RO:0002575 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002583 +name: existence starts at end of +def: "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." [] +is_a: RO:0002496 ! existence starts during or after + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: BFO:0000051 RO:0002215 +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002585 +name: results in closure of +property_value: IAO:0000116 "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." xsd:string +is_a: RO:0002295 ! results in developmental progression of +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002586 +name: results in breakdown of +def: "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" [] +is_a: RO:0002233 ! has input + +[Typedef] +id: RO:0002587 +name: results in synthesis of +is_a: RO:0002297 ! results in formation of + +[Typedef] +id: RO:0002588 +name: results in assembly of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002297 ! results in formation of +is_a: RO:0002592 ! results in organization of + +[Typedef] +id: RO:0002589 +name: results in catabolism of +def: "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." [] +is_a: RO:0002586 ! results in breakdown of + +[Typedef] +id: RO:0002590 +name: results in disassembly of +is_a: RO:0002586 ! results in breakdown of +is_a: RO:0002592 ! results in organization of + +[Typedef] +id: RO:0002591 +name: results in remodeling of +is_a: RO:0002233 ! has input +is_a: RO:0002592 ! results in organization of + +[Typedef] +id: RO:0002592 +name: results in organization of +def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] +is_a: RO:0040036 ! results in changes to anatomical or cellular structure + +[Typedef] +id: RO:0002593 +name: existence ends at start of +def: "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." [] +is_a: RO:0002497 ! existence ends during or before + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002596 +name: capable of regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002211 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +name: capable of negatively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002212 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +name: capable of positively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002213 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002599 +name: capable of inhibiting or preventing pathological process +def: "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." [] +property_value: IAO:0000112 "pazopanib -> pathological angiogenesis" xsd:string +property_value: IAO:0000118 "treats" xsd:string {comment="Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship"} +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." xsd:string +is_a: RO:0002597 ! capable of negatively regulating + +[Typedef] +id: RO:0002600 +name: capable of upregulating or causing pathological process +def: "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." [] +property_value: IAO:0000112 "benzene -> cancer [CHEBI]" xsd:string +property_value: IAO:0000118 "causes disease" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002598 ! capable of positively regulating + +[Typedef] +id: RO:0002606 +name: is substance that treats +def: "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." [] +property_value: IAO:0000118 "treats" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: seeAlso https://code.google.com/p/obo-relations/issues/detail?id=46 +is_a: RO:0002599 ! capable of inhibiting or preventing pathological process + +[Typedef] +id: RO:0002607 +name: is marker for +def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." [] +property_value: IAO:0000116 "May be ceded to OBI" xsd:string +is_a: RO:0002610 ! correlated with + +[Typedef] +id: RO:0002608 +name: process has causal agent +def: "Inverse of 'causal agent in process'" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002609 +name: obsolete related via dependence to +def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +is_obsolete: true + +[Typedef] +id: RO:0002610 +name: correlated with +def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] +property_value: IAO:0000232 "Groups both positive and negative correlation" xsd:string + +[Typedef] +id: RO:0002614 +name: is evidence with support from +def: "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." [] +comment: In the Gene Ontology association model, this corresponds to the With/From field +property_value: IAO:0000112 "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." xsd:string +is_a: RO:0002616 ! related via evidence or inference to + +[Typedef] +id: RO:0002615 +name: has model +def: "Inverse of is-model-of" [] +inverse_of: RO:0003301 ! has role in modeling + +[Typedef] +id: RO:0002616 +name: related via evidence or inference to +property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string + +[Typedef] +id: RO:0002618 +name: visits +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI +is_a: RO:0002574 ! participates in a biotic-biotic interaction with +inverse_of: RO:0002619 ! visited by + +[Typedef] +id: RO:0002619 +name: visited by +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002622 +name: visits flowers of +is_a: RO:0002618 ! visits +inverse_of: RO:0002623 ! has flowers visited by + +[Typedef] +id: RO:0002623 +name: has flowers visited by +is_a: RO:0002619 ! visited by + +[Typedef] +id: RO:0002624 +name: lays eggs in +is_a: RO:0002444 ! parasite of +is_a: RO:0002618 ! visits +inverse_of: RO:0002625 ! has eggs laid in by + +[Typedef] +id: RO:0002625 +name: has eggs laid in by +is_a: RO:0002445 ! parasitized by +is_a: RO:0002619 ! visited by + +[Typedef] +id: RO:0002626 +name: kills +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string +is_a: RO:0002574 ! participates in a biotic-biotic interaction with +inverse_of: RO:0002627 ! is killed by + +[Typedef] +id: RO:0002627 +name: is killed by +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002629 +name: directly positively regulates +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string +property_value: RO:0004049 RO:0002578 +is_a: RO:0002213 ! positively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002630 +name: directly negatively regulates +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string +property_value: RO:0004050 RO:0002578 +is_a: RO:0002212 ! negatively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002632 +name: ectoparasite of +def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] +property_value: IAO:0000119 Types +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002633 ! has ectoparasite + +[Typedef] +id: RO:0002633 +name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002634 +name: endoparasite of +synonym: "lives inside of" RELATED [] +property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string +property_value: IAO:0000119 Types +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002635 ! has endoparasite + +[Typedef] +id: RO:0002635 +name: has endoparasite +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002636 +name: mesoparasite of +def: "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" [] +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002637 ! has mesoparasite + +[Typedef] +id: RO:0002637 +name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002638 +name: intercellular endoparasite of +def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] +property_value: IAO:0000119 Types +is_a: RO:0002634 ! endoparasite of +inverse_of: RO:0002639 ! has intercellular endoparasite + +[Typedef] +id: RO:0002639 +name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 +is_a: RO:0002635 ! has endoparasite + +[Typedef] +id: RO:0002640 +name: intracellular endoparasite of +def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] +property_value: IAO:0000119 Types +is_a: RO:0002634 ! endoparasite of +inverse_of: RO:0002641 ! has intracellular endoparasite + +[Typedef] +id: RO:0002641 +name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 +is_a: RO:0002635 ! has endoparasite + +[Typedef] +id: RO:0002801 +name: co-roosts with +def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] +property_value: IAO:0000119 Communal:roosting +is_symmetric: true +is_a: RO:0008506 ! ecologically co-occurs with + +[Typedef] +id: RO:0003000 +name: produces +def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] +comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +inverse_of: RO:0003001 ! produced by + +[Typedef] +id: RO:0003001 +name: produced by +def: "a produced_by b iff some process that occurs_in b has_output a." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity + +[Typedef] +id: RO:0003002 +name: represses expression of +def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002449 ! directly negatively regulates activity of + +[Typedef] +id: RO:0003003 +name: increases expression of +def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002450 ! directly positively regulates activity of + +[Typedef] +id: RO:0003301 +name: has role in modeling +def: "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] +comment: The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. +property_value: IAO:0000117 https://orcid.org/0000-0002-1048-5019 +property_value: IAO:0000118 "is used to study" xsd:string +is_asymmetric: true + +[Typedef] +id: RO:0003302 +name: causes or contributes to condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. +property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." xsd:string +property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0003303 +name: causes condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003304 +name: contributes to condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." [] +is_a: RO:0003302 ! causes or contributes to condition + +[Typedef] +id: RO:0003305 +name: contributes to severity of condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." [] +property_value: IAO:0000118 "contributes to expressivity of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003306 +name: contributes to frequency of condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." [] +property_value: IAO:0000118 "contributes to penetrance of condition" xsd:string +is_a: RO:0003304 ! contributes to condition + +[Typedef] +id: RO:0003307 +name: ameliorates condition +def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." [] +comment: Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. +property_value: IAO:0000118 "is preventative for condition" xsd:string +is_a: RO:0003305 ! contributes to severity of condition + +[Typedef] +id: RO:0003308 +name: correlated with condition +def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] +is_a: RO:0002610 ! correlated with + +[Typedef] +id: RO:0003309 +name: exacerbates condition +def: "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." [] +is_a: RO:0003305 ! contributes to severity of condition + +[Typedef] +id: RO:0003310 +name: condition ameliorated by +def: "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." [] +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0003311 +name: condition exacerbated by +def: "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." [] +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0004000 +name: condition has genetic basis in +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string +domain: BFO:0000017 ! realizable entity +is_a: RO:0002410 ! causally related to +inverse_of: RO:0004010 ! is genetic basis for condition +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:38:20Z + +[Typedef] +id: RO:0004001 +name: has material basis in gain of function germline mutation in +property_value: seeAlso Orphanet:410295 +property_value: seeAlso Orphanet:410296 +is_a: RO:0004000 ! condition has genetic basis in +inverse_of: RO:0004011 ! is causal gain of function germline mutation of in +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:45:20Z + +[Typedef] +id: RO:0004002 +name: has material basis in loss of function germline mutation in +is_a: RO:0004000 ! condition has genetic basis in +inverse_of: RO:0004012 ! is causal loss of function germline mutation of in +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:45:37Z + +[Typedef] +id: RO:0004003 +name: has material basis in germline mutation in +property_value: seeAlso Orphanet:317343 +is_a: RO:0004000 ! condition has genetic basis in +inverse_of: RO:0004013 ! is causal germline mutation in +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:45:54Z + +[Typedef] +id: RO:0004004 +name: has material basis in somatic mutation in +property_value: seeAlso Orphanet:317344 +is_a: RO:0004000 ! condition has genetic basis in +inverse_of: RO:0004014 ! is causal somatic mutation in +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:46:07Z + +[Typedef] +id: RO:0004005 +name: has major susceptibility factor +is_a: RO:0004000 ! condition has genetic basis in +inverse_of: RO:0004015 ! is causal susceptibility factor for +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:46:26Z + +[Typedef] +id: RO:0004006 +name: has partial material basis in germline mutation in +is_a: RO:0004000 ! condition has genetic basis in +inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:46:57Z + +[Typedef] +id: RO:0004007 +name: has primary input or output +def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +is_a: RO:0000057 ! has participant +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-12-13T11:26:17Z + +[Typedef] +id: RO:0004008 +name: has primary output +def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +is_a: RO:0002234 ! has output +is_a: RO:0004007 ! has primary input or output +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-12-13T11:26:32Z + +[Typedef] +id: RO:0004009 +name: has primary input +def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +is_a: RO:0002233 ! has input +is_a: RO:0004007 ! has primary input or output +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-12-13T11:26:56Z + +[Typedef] +id: RO:0004010 +name: is genetic basis for condition +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a more specific relations" xsd:string +range: BFO:0000017 ! realizable entity +is_a: RO:0004018 ! is basis for realizable +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:53:08Z + +[Typedef] +id: RO:0004011 +name: is causal gain of function germline mutation of in +def: "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] +property_value: seeAlso Orphanet:410296 +is_a: RO:0004010 ! is genetic basis for condition +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:55:51Z + +[Typedef] +id: RO:0004012 +name: is causal loss of function germline mutation of in +def: "Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] +property_value: seeAlso Orphanet:410295 +is_a: RO:0004010 ! is genetic basis for condition +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:56:06Z + +[Typedef] +id: RO:0004013 +name: is causal germline mutation in +def: "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] +property_value: seeAlso Orphanet:317343 +is_a: RO:0003303 ! causes condition +is_a: RO:0004010 ! is genetic basis for condition +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:56:40Z + +[Typedef] +id: RO:0004014 +name: is causal somatic mutation in +def: "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." [] +property_value: seeAlso Orphanet:317344 +is_a: RO:0003303 ! causes condition +is_a: RO:0004010 ! is genetic basis for condition +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:57:07Z + +[Typedef] +id: RO:0004015 +name: is causal susceptibility factor for +def: "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." [] +property_value: seeAlso Orphanet:317345 +is_a: RO:0004010 ! is genetic basis for condition +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:57:43Z + +[Typedef] +id: RO:0004016 +name: is causal germline mutation partially giving rise to +def: "Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]." [] +property_value: seeAlso Orphanet:317346 +is_a: RO:0003304 ! contributes to condition +is_a: RO:0004010 ! is genetic basis for condition +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T02:58:43Z + +[Typedef] +id: RO:0004017 +name: realizable has basis in +is_a: RO:0002410 ! causally related to +inverse_of: RO:0004018 ! is basis for realizable +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T03:20:01Z + +[Typedef] +id: RO:0004018 +name: is basis for realizable +is_a: RO:0002410 ! causally related to +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T03:20:29Z + +[Typedef] +id: RO:0004019 +name: disease has basis in +domain: OGMS:0000031 ! disease +is_a: RO:0004017 ! realizable has basis in +is_a: RO:0004023 ! causal relationship with disease as subject +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T03:26:47Z + +[Typedef] +id: RO:0004020 +name: disease has basis in dysfunction of +def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] +property_value: IAO:0000589 "disease has basis in dysfunction of (disease to anatomical structure)" xsd:string +range: CARO:0000006 ! material anatomical entity +is_a: RO:0004019 ! disease has basis in +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T03:29:32Z + +[Typedef] +id: RO:0004021 +name: disease has basis in disruption of +def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] +property_value: IAO:0000589 "disease has basis in disruption of (disease to process)" xsd:string +range: BFO:0000015 ! process +is_a: RO:0004019 ! disease has basis in +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T03:37:52Z + +[Typedef] +id: RO:0004022 +name: disease has basis in feature +def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] +domain: OGMS:0000031 ! disease +is_a: RO:0002200 ! has phenotype +is_a: RO:0004019 ! disease has basis in +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T03:46:07Z + +[Typedef] +id: RO:0004023 +name: causal relationship with disease as subject +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." xsd:string +domain: OGMS:0000031 ! disease +is_a: RO:0002410 ! causally related to +is_a: RO:0040035 ! disease relationship +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T03:50:54Z + +[Typedef] +id: RO:0004024 +name: disease causes disruption of +def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] +property_value: IAO:0000589 "disease causes disruption of (disease to process)" xsd:string +domain: OGMS:0000031 ! disease +range: BFO:0000015 ! process +holds_over_chain: RO:0004025 RO:0002215 +is_a: RO:0004023 ! causal relationship with disease as subject +transitive_over: BFO:0000050 ! part of +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T03:51:09Z + +[Typedef] +id: RO:0004025 +name: disease causes dysfunction of +property_value: IAO:0000589 "disease causes dysfunction of (disease to anatomical entity)" xsd:string +domain: OGMS:0000031 ! disease +range: CARO:0000006 ! material anatomical entity +is_a: RO:0004023 ! causal relationship with disease as subject +transitive_over: BFO:0000050 ! part of +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T03:58:20Z + +[Typedef] +id: RO:0004026 +name: disease has location +def: "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." [] +property_value: IAO:0000116 "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" xsd:string +property_value: IAO:0000232 "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." xsd:string +domain: OGMS:0000031 ! disease +range: BFO:0000004 ! independent continuant +is_a: RO:0040035 ! disease relationship +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-11-05T04:06:02Z + +[Typedef] +id: RO:0004027 +name: disease has inflammation site +def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] +domain: OGMS:0000031 ! disease +range: BFO:0000004 ! independent continuant +is_a: RO:0004026 ! disease has location +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-12-26T19:37:31Z + +[Typedef] +id: RO:0004028 +name: realized in response to stimulus +def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] +domain: BFO:0000017 ! realizable entity +range: BFO:0000040 ! material entity +holds_over_chain: RO:0009501 RO:0002233 +is_a: RO:0002410 ! causally related to +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-12-26T19:45:49Z + +[Typedef] +id: RO:0004029 +name: disease has feature +def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] +domain: OGMS:0000031 ! disease +is_a: RO:0040035 ! disease relationship +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-12-26T19:50:53Z + +[Typedef] +id: RO:0004030 +name: disease arises from alteration in structure +def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] +range: CARO:0000003 ! connected anatomical structure +is_a: RO:0004019 ! disease has basis in +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2017-12-26T19:58:44Z + +[Typedef] +id: RO:0004031 +name: enables subfunction +def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] +holds_over_chain: RO:0002327 BFO:0000051 +is_a: RO:0002328 ! functionally related to +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-25T23:20:13Z + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 RO:0002304 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 RO:0002305 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: RO:0004050 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: RO:0004049 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-03-13T23:55:19Z + +[Typedef] +id: RO:0004096 +name: DEPRECATED inheres in +comment: DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. +is_obsolete: true + +[Typedef] +id: RO:0004097 +name: DEPRECATED bearer of +is_obsolete: true + +[Typedef] +id: RO:0007000 +name: has driver +def: "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8910-9851 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/506 + +[Typedef] +id: RO:0007001 +name: has disease driver +def: "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8910-9851 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/506 +is_a: RO:0007000 ! has driver + +[Typedef] +id: RO:0008501 +name: epiphyte of +def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string +is_a: RO:0002440 ! symbiotically interacts with +inverse_of: RO:0008502 ! has epiphyte + +[Typedef] +id: RO:0008502 +name: has epiphyte +def: "inverse of epiphyte of" [] +subset: RO:0002259 +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0008503 +name: kleptoparasite of +def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string +is_a: RO:0002444 ! parasite of +inverse_of: RO:0008504 ! kleptoparasitized by + +[Typedef] +id: RO:0008504 +name: kleptoparasitized by +def: "inverse of kleptoparasite of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0008505 +name: creates habitat for +def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] +domain: CARO:0001010 ! organism or virus or viroid +range: CARO:0001010 ! organism or virus or viroid +is_a: RO:0002321 ! ecologically related to + +[Typedef] +id: RO:0008506 +name: ecologically co-occurs with +def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] +domain: CARO:0001010 ! organism or virus or viroid +range: CARO:0001010 ! organism or virus or viroid +is_symmetric: true +is_a: RO:0002321 ! ecologically related to + +[Typedef] +id: RO:0008507 +name: lays eggs on +def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] +is_a: RO:0002618 ! visits +inverse_of: RO:0008508 ! has eggs laid on by + +[Typedef] +id: RO:0008508 +name: has eggs laid on by +def: "inverse of lays eggs on" [] +is_a: RO:0002619 ! visited by + +[Typedef] +id: RO:0009001 +name: has substance added +def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." [] +property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity + +[Typedef] +id: RO:0009002 +name: has substance removed +def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] +property_value: IAO:0000112 "'egg white' 'has substance removed' some 'egg yolk'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity + +[Typedef] +id: RO:0009003 +name: immersed in +def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] +property_value: IAO:0000112 "sardines 'immersed in' some 'oil and mustard'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity + +[Typedef] +id: RO:0009004 +name: has consumer +def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] +property_value: IAO:0000112 "sardine has consumer some homo sapiens" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 +domain: BFO:0000040 ! material entity +range: CARO:0001010 ! organism or virus or viroid + +[Typedef] +id: RO:0009005 +name: has primary substance added +def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] +property_value: IAO:0000112 "bread 'has primary substance added' some 'flour'" xsd:string +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 +is_a: RO:0009001 ! has substance added + +[Typedef] +id: RO:0009501 +name: realized in response to +def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] +synonym: "triggered by process" EXACT [RO:cjm] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 +property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string +property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string +property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI +domain: BFO:0000017 ! realizable entity +range: BFO:0000015 ! process +holds_over_chain: BFO:0000054 RO:0002404 +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0010001 +name: generically depends on +def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] +synonym: "g-depends on" EXACT [] +property_value: IAO:0000112 "Genetic information generically depend on molecules of DNA." xsd:string +property_value: IAO:0000112 "The novel *War and Peace* generically depends on this copy of the novel." xsd:string +property_value: IAO:0000112 "The pattern shared by chess boards generically depends on any chess board." xsd:string +property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string +property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000031 ! generically dependent continuant +range: BFO:0000004 ! independent continuant +holds_over_chain: RO:0000052 RO:0000058 +inverse_of: RO:0010002 ! is carrier of + +[Typedef] +id: RO:0010002 +name: is carrier of +def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] +property_value: IAO:0000112 "Molecules of DNA are carriers of genetic information." xsd:string +property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string +property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string +property_value: IAO:0000119 "[072-ISO]" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000031 ! generically dependent continuant +holds_over_chain: RO:0000059 RO:0000053 + +[Typedef] +id: RO:0011002 +name: regulates activity of +def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002566 ! causally influences + +[Typedef] +id: RO:0011003 +name: regulates quantity of +def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002566 ! causally influences + +[Typedef] +id: RO:0011004 +name: indirectly regulates activity of +def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0011002 ! regulates activity of + +[Typedef] +id: RO:0011007 +name: decreases by repression quantity of +def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0011023 ! indirectly negatively regulates quantity of + +[Typedef] +id: RO:0011008 +name: increases by expression quantity of +def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0011024 ! indirectly positively regulates quantity of + +[Typedef] +id: RO:0011009 +name: directly positively regulates quantity of +def: "The entity A has an activity that directly positively regulates the quantity of B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0011021 ! directly regulates quantity of + +[Typedef] +id: RO:0011010 +name: directly negatively regulates quantity of +def: "The entity A has an activity that directly negatively regulates the quantity of B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0011021 ! directly regulates quantity of + +[Typedef] +id: RO:0011013 +name: indirectly positively regulates activity of +def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000118 "indirectly activates" xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0011004 ! indirectly regulates activity of + +[Typedef] +id: RO:0011014 +name: destabilizes quantity of +def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] +property_value: IAO:0000112 "AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0011010 ! directly negatively regulates quantity of + +[Typedef] +id: RO:0011015 +name: stabilizes quantity of +def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] +property_value: IAO:0000112 "AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0011009 ! directly positively regulates quantity of + +[Typedef] +id: RO:0011016 +name: indirectly negatively regulates activity of +def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +property_value: IAO:0000118 "indirectly inhibits" xsd:string +is_a: RO:0011004 ! indirectly regulates activity of + +[Typedef] +id: RO:0011021 +name: directly regulates quantity of +def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +is_a: RO:0011003 ! regulates quantity of + +[Typedef] +id: RO:0011022 +name: indirectly regulates quantity of +def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +is_a: RO:0011003 ! regulates quantity of + +[Typedef] +id: RO:0011023 +name: indirectly negatively regulates quantity of +def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +is_a: RO:0011022 ! indirectly regulates quantity of + +[Typedef] +id: RO:0011024 +name: indirectly positively regulates quantity of +def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 +is_a: RO:0011022 ! indirectly regulates quantity of + +[Typedef] +id: RO:0012000 +name: has small molecule regulator +def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] +is_a: RO:0000057 ! has participant +inverse_of: RO:0012004 ! is small molecule regulator of +created_by: pg +creation_date: 2020-04-22T20:27:26Z + +[Typedef] +id: RO:0012001 +name: has small molecule activator +def: "a relation between a process and a continuant, in which the process is activated by the small molecule continuant" [] +is_a: RO:0012000 ! has small molecule regulator +inverse_of: RO:0012005 ! is small molecule activator of +created_by: pg +creation_date: 2020-04-22T20:28:37Z + +[Typedef] +id: RO:0012002 +name: has small molecule inhibitor +def: "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant" [] +is_a: RO:0012000 ! has small molecule regulator +inverse_of: RO:0012006 ! is small molecule inhibitor of +created_by: pg +creation_date: 2020-04-22T20:28:54Z + +[Typedef] +id: RO:0012003 +name: acts on population of +def: "p acts on population of c iff c' is a collection, has members of type c, and p has participant c" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0000057 ! has participant +created_by: pg +creation_date: 2020-06-08T17:21:33Z + +[Typedef] +id: RO:0012004 +name: is small molecule regulator of +def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] +is_a: RO:0002596 ! capable of regulating +created_by: pg +creation_date: 2020-06-24T13:15:17Z + +[Typedef] +id: RO:0012005 +name: is small molecule activator of +def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] +is_a: RO:0002598 ! capable of positively regulating +is_a: RO:0012004 ! is small molecule regulator of +created_by: pg +creation_date: 2020-06-24T13:15:26Z + +[Typedef] +id: RO:0012006 +name: is small molecule inhibitor of +def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] +is_a: RO:0002597 ! capable of negatively regulating +is_a: RO:0012004 ! is small molecule regulator of +created_by: pg +creation_date: 2020-06-24T13:15:35Z + +[Typedef] +id: RO:0012007 +name: results in adhesion of +def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] +is_a: RO:0040036 ! results in changes to anatomical or cellular structure +created_by: pg +creation_date: 2020-08-27T08:13:59Z + +[Typedef] +id: RO:0012008 +name: results in fusion of +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002592 ! results in organization of +created_by: pg +creation_date: 2021-02-26T07:28:29Z + +[Typedef] +id: RO:0012009 +name: constitutively upstream of +def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002304 ! causally upstream of, positive effect +created_by: pg +creation_date: 2022-09-26T06:01:01Z + +[Typedef] +id: RO:0012010 +name: removes input for +def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +is_a: RO:0002305 ! causally upstream of, negative effect +created_by: pg +creation_date: 2022-09-26T06:06:20Z + +[Typedef] +id: RO:0012011 +name: indirectly causally upstream of +def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] +is_a: RO:0002411 ! causally upstream of +created_by: pg +creation_date: 2022-09-26T06:07:17Z + +[Typedef] +id: RO:0012012 +name: indirectly regulates +def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] +is_a: RO:0002211 ! regulates +is_a: RO:0012011 ! indirectly causally upstream of +created_by: pg +creation_date: 2022-09-26T06:08:01Z + +[Typedef] +id: RO:0013001 +name: has synaptic IO in region +def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] +synonym: "has synaptic input or output in" EXACT [] +is_a: RO:0002130 ! has synaptic terminal in +transitive_over: BFO:0000050 ! part of +created_by: http://orcid.org/0000-0002-1373-1705 +creation_date: 2020-07-17T09:26:52Z + +[Typedef] +id: RO:0013002 +name: receives synaptic input in region +def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region." [] +is_a: RO:0002110 ! has postsynaptic terminal in +is_a: RO:0013001 ! has synaptic IO in region +transitive_over: BFO:0000050 ! part of +created_by: http://orcid.org/0000-0002-1373-1705 +creation_date: 2020-07-17T09:42:23Z + +[Typedef] +id: RO:0013003 +name: sends synaptic output to region +def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region." [] +is_a: RO:0002113 ! has presynaptic terminal in +is_a: RO:0013001 ! has synaptic IO in region +transitive_over: BFO:0000050 ! part of +created_by: http://orcid.org/0000-0002-1373-1705 +creation_date: 2020-07-17T09:45:06Z + +[Typedef] +id: RO:0013004 +name: has synaptic IO throughout +def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] +is_a: RO:0013001 ! has synaptic IO in region +created_by: http://orcid.org/0000-0002-1373-1705 +creation_date: 2020-07-17T09:52:19Z + +[Typedef] +id: RO:0013005 +name: receives synaptic input throughout +def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." [] +is_a: RO:0013002 ! receives synaptic input in region +is_a: RO:0013004 ! has synaptic IO throughout +created_by: http://orcid.org/0000-0002-1373-1705 +creation_date: 2020-07-17T09:55:36Z + +[Typedef] +id: RO:0013006 +name: sends synaptic output throughout +def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." [] +is_a: RO:0013003 ! sends synaptic output to region +is_a: RO:0013004 ! has synaptic IO throughout +created_by: http://orcid.org/0000-0002-1373-1705 +creation_date: 2020-07-17T09:57:27Z + +[Typedef] +id: RO:0013007 +name: has sensory dendrite in +def: "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." [] +synonym: "has sensory dendrite location" EXACT [] +synonym: "has sensory terminal in" EXACT [] +synonym: "has sensory terminal location" EXACT [] +domain: CL:0000101 ! sensory neuron +is_a: RO:0002360 ! has dendrite location +transitive_over: BFO:0000050 ! part of +created_by: http://orcid.org/0000-0002-1373-1705 +creation_date: 2020-07-20T12:10:09Z + +[Typedef] +id: RO:0013008 +name: receives synaptic input from neuron +def: "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." [] +is_a: RO:0002103 ! synapsed by +inverse_of: RO:0013009 ! sends synaptic output to cell +created_by: http://orcid.org/0000-0002-1373-1705 +creation_date: 2021-05-26T08:40:18Z + +[Typedef] +id: RO:0013009 +name: sends synaptic output to cell +def: "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." [] +comment: Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. +is_a: RO:0002120 ! synapsed to +created_by: http://orcid.org/0000-0002-1373-1705 +creation_date: 2021-05-26T08:41:07Z + +[Typedef] +id: RO:0014001 +name: disease has infectious agent +def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] +is_a: RO:0004019 ! disease has basis in +created_by: http://orcid.org/0000-0001-5208-3432 + +[Typedef] +id: RO:0015001 +name: has exemplar data +def: "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." [] +property_value: IAO:0000112 "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" xsd:string +property_value: IAO:0000116 "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 +property_value: IAO:0000232 "This relation is not meant to capture the relation between occurrents and data." xsd:string +inverse_of: RO:0015002 ! exemplar data of +transitive_over: RO:0015003 ! subcluster of + +[Typedef] +id: RO:0015002 +name: exemplar data of +property_value: IAO:0000117 https://orcid.org/0000-0002-5260-9315 + +[Typedef] +id: RO:0015003 +name: subcluster of +def: "A relation between a group and another group it is part of but does not fully constitute." [] +property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 +property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string +is_transitive: true +is_a: BFO:0000050 ! part of + +[Typedef] +id: RO:0015004 +name: has characterizing marker set +def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] +synonym: "has marker gene combination" EXACT [] +synonym: "has marker signature set" EXACT [] +property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-7258-9596 +property_value: IAO:0000112 "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." xsd:string +property_value: IAO:0000112 "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." xsd:string +property_value: IAO:0000116 "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." xsd:string +property_value: IAO:0000232 "This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context." xsd:string +domain: CL:0000000 ! cell + +[Typedef] +id: RO:0015006 +name: different in magnitude relative to +def: "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality + +[Typedef] +id: RO:0015007 +name: increased in magnitude relative to +def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_a: RO:0015006 ! different in magnitude relative to + +[Typedef] +id: RO:0015008 +name: decreased in magnitude relative to +def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_a: RO:0015006 ! different in magnitude relative to + +[Typedef] +id: RO:0015009 +name: similar in magnitude relative to +def: "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] + +[Typedef] +id: RO:0015010 +name: has relative magnitude + +[Typedef] +id: RO:0015011 +name: has cross section +def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [https://orcid.org/0000-0002-6601-2165] +comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. + +[Typedef] +id: RO:0015012 +name: reciprocal of +def: "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e." [https://orcid.org/0000-0002-6601-2165] +comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + +[Typedef] +id: RO:0015015 +name: has high plasma membrane amount +def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string +domain: CL:0000000 ! cell +is_a: RO:0002104 ! has plasma membrane part + +[Typedef] +id: RO:0015016 +name: has low plasma membrane amount +def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-1940-6740 +property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string +domain: CL:0000000 ! cell +is_a: RO:0002104 ! has plasma membrane part + +[Typedef] +id: RO:0016001 +name: has phenotype or disease +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string + +[Typedef] +id: RO:0016002 +name: has disease +def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] +property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string +is_a: RO:0016001 ! has phenotype or disease + +[Typedef] +id: RO:0016004 +name: has exposure medium +def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string +is_a: RO:0002244 ! related via exposure to +created_by: https://orcid.org/0000-0002-7463-6306 + +[Typedef] +id: RO:0017001 +name: device utilizes material +def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] +synonym: "utilizes" BROAD [] +property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 +property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 +property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string +property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string +holds_over_chain: RO:0002215 RO:0002233 +creation_date: 2021-11-08T12:00:00Z + +[Typedef] +id: RO:0018001 +name: is myristoyltransferase activity +def: "Helper relation for OWL definition of RO:0018002 myristoylates" [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4423-4370 +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0018002 +name: myristoylates +def: "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" [] +property_value: http://purl.org/dc/terms/conformsTo http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4423-4370 +is_a: RO:0002436 ! molecularly interacts with +inverse_of: RO:0018003 ! myristoylated by + +[Typedef] +id: RO:0018003 +name: myristoylated by +def: "inverse of myristoylates" [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4423-4370 + +[Typedef] +id: RO:0018027 +name: is agonist of +def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" xsd:string +property_value: seeAlso https://www.wikidata.org/wiki/Property:P3772 +is_a: RO:0002450 ! directly positively regulates activity of + +[Typedef] +id: RO:0018028 +name: is inverse agonist of +def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" xsd:string +property_value: seeAlso https://www.wikidata.org/wiki/Property:P9275 +is_a: RO:0002449 ! directly negatively regulates activity of + +[Typedef] +id: RO:0018029 +name: is antagonist of +def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] +property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-4423-4370 +property_value: IAO:0000112 "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" xsd:string +property_value: seeAlso https://www.wikidata.org/wiki/Property:P3773 +is_a: RO:0002449 ! directly negatively regulates activity of + +[Typedef] +id: RO:0019000 +name: regulates characteristic +def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +domain: BFO:0000015 ! process +range: PATO:0000001 ! quality +holds_over_chain: RO:0002211 RO:0019000 +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0019001 +name: positively regulates characteristic +def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +holds_over_chain: RO:0002213 RO:0019001 +is_a: RO:0019000 ! regulates characteristic + +[Typedef] +id: RO:0019002 +name: negatively regulates characteristic +def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +holds_over_chain: RO:0002212 RO:0019001 +holds_over_chain: RO:0002213 RO:0019002 +is_a: RO:0019000 ! regulates characteristic + +[Typedef] +id: RO:0019501 +name: confers susceptibility to condition +def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] +is_a: RO:0003304 ! contributes to condition +created_by: http://orcid.org/0000-0002-4142-7153 + +[Typedef] +id: RO:0040035 +name: disease relationship +def: "This relation groups relations between diseases and any other kind of entity." [] +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." xsd:string +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-09-26T00:00:32Z + +[Typedef] +id: RO:0040036 +name: results in changes to anatomical or cellular structure +def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] +is_a: RO:0000057 ! has participant +created_by: https://orcid.org/0000-0002-6601-2165 +creation_date: 2018-09-26T01:08:58Z + +[Typedef] +id: RO:HOM0000000 +name: in similarity relationship with +def: "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000000] +synonym: "correspondence" RELATED [http://dx.doi.org/10.1007/BF02814479] +synonym: "resemblance" RELATED [] +synonym: "sameness" EXACT [] +synonym: "similar to" EXACT [] +xref: ECO:0000041 +xref: SO:similar_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: IAO:0000116 "TODO: Add homeomorphy axiom" xsd:string +property_value: RO:0040042 BFO:0000002 +property_value: RO:0040042 BFO:0000003 +property_value: seeAlso HOM:0000000 +is_symmetric: true + +[Typedef] +id: RO:HOM0000001 +name: in homology relationship with +def: "Similarity that results from common evolutionary origin." [http://dx.doi.org/10.1002/bies.950180611, http://dx.doi.org/10.1002/jmor.1051730307, http://dx.doi.org/10.1007/BF02814480, http://purl.obolibrary.org/obo/HOM_0000001] +comment: This broad definition encompasses all the working definitions proposed so far in the literature. +synonym: "homologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000001 +is_symmetric: true +is_a: RO:0002158 ! shares ancestor with +is_a: RO:HOM0000000 ! in similarity relationship with +disjoint_from: RO:HOM0000002 ! in homoplasy relationship with + +[Typedef] +id: RO:HOM0000002 +name: in homoplasy relationship with +def: "Similarity that results from independent evolution." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000002] +synonym: "analogy" RELATED [] +synonym: "homoplasous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000002 +is_symmetric: true +is_a: RO:HOM0000000 ! in similarity relationship with + +[Typedef] +id: RO:HOM0000003 +name: in homocracy relationship with +def: "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/s00427-003-0301-4, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000003] +comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. +synonym: "homocracous to" EXACT [] +xref: ECO:0000075 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000003 +is_symmetric: true +is_a: RO:0002320 ! evolutionarily related to +is_a: RO:HOM0000000 ! in similarity relationship with + +[Typedef] +id: RO:HOM0000004 +name: in convergence relationship with +def: "Homoplasy that involves different underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000004] +comment: Convergence usually implies a notion of adaptation. +synonym: "analogy" RELATED [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000004 +is_symmetric: true +is_a: RO:HOM0000002 ! in homoplasy relationship with + +[Typedef] +id: RO:HOM0000005 +name: in parallelism relationship with +def: "Homoplasy that involves homologous underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000005] +comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. +synonym: "parallel evolution" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000005 +is_symmetric: true +is_a: RO:HOM0000002 ! in homoplasy relationship with + +[Typedef] +id: RO:HOM0000006 +name: in structural homology relationship with +def: "Homology that is defined by similarity with regard to selected structural parameters." [http://dx.doi.org/10.1016/j.jhevol.2006.11.014, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000006, ISBN:0123195837] +synonym: "idealistic homology" RELATED [] +synonym: "structural homologous to" EXACT [] +xref: ECO:0000071 +xref: MI:2163 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000006 +is_symmetric: true +is_a: RO:HOM0000001 ! in homology relationship with + +[Typedef] +id: RO:HOM0000007 +name: in historical homology relationship with +def: "Homology that is defined by common descent." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://purl.obolibrary.org/obo/HOM_0000007, ISBN:0123195837] +synonym: "cladistic homology" EXACT [] +synonym: "historical homologous to" EXACT [] +synonym: "homology" BROAD [] +synonym: "phylogenetic homology" EXACT [] +synonym: "taxic homology" EXACT [] +synonym: "true homology" RELATED [] +xref: ECO:0000080 +xref: RO_proposed_relation:homologous_to +xref: SO:0000330 +xref: SO:0000853 +xref: SO:0000857 +xref: SO:homologous_to +xref: TAO:homologous_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000007 +is_symmetric: true +is_a: RO:HOM0000001 ! in homology relationship with + +[Typedef] +id: RO:HOM0000008 +name: in biological homology relationship with +def: "Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000008] +comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. +synonym: "biological homologous to" EXACT [] +synonym: "transformational homology" RELATED [] +xref: ECO:0000067 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000008 +is_symmetric: true +is_a: RO:HOM0000001 ! in homology relationship with + +[Typedef] +id: RO:HOM0000009 +name: in reversal relationship with +def: "Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000009] +synonym: "atavism" EXACT [] +synonym: "reversion" RELATED [] +synonym: "rudiment" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000009 +is_symmetric: true +is_a: RO:HOM0000002 ! in homoplasy relationship with + +[Typedef] +id: RO:HOM0000010 +name: in syntenic homology relationship with +def: "Structural homology that is detected by similarity in content and organization between chromosomes." [http://purl.obolibrary.org/obo/HOM_0000010, MeSH:Synteny] +synonym: "syntenic homologous to" EXACT [] +synonym: "synteny" RELATED [] +xref: MeSH:Synteny +xref: SO:0000860 +xref: SO:0005858 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000010 +is_symmetric: true +is_a: RO:HOM0000006 ! in structural homology relationship with + +[Typedef] +id: RO:HOM0000011 +name: in paralogy relationship with +def: "Historical homology that involves genes that diverged after a duplication event." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000011, http://www.ncbi.nlm.nih.gov/pubmed/5449325] +synonym: "paralogous to" EXACT [] +xref: SO:0000854 +xref: SO:0000859 +xref: SO:paralogous_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000011 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with +disjoint_from: RO:HOM0000017 ! in orthology relationship with + +[Typedef] +id: RO:HOM0000012 +name: in syntenic paralogy relationship with +def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20001215)288\:4<345\:\:AID-JEZ7>3.0.CO;2-Y, http://dx.doi.org/10.1186/1471-213X-7-100, http://purl.obolibrary.org/obo/HOM_0000012] +synonym: "duplicon" RELATED [] +synonym: "paralogon" RELATED [] +synonym: "syntenic paralogous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000012 +is_symmetric: true +is_a: RO:HOM0000010 ! in syntenic homology relationship with +is_a: RO:HOM0000011 ! in paralogy relationship with + +[Typedef] +id: RO:HOM0000013 +name: in syntenic orthology relationship with +def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] +synonym: "syntenic orthologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000013 +is_symmetric: true +is_a: RO:HOM0000010 ! in syntenic homology relationship with + +[Typedef] +id: RO:HOM0000014 +name: in partial homology relationship with +def: "Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous." [http://purl.obolibrary.org/obo/HOM_0000014, ISBN:0123195837, ISBN:978-0471984931] +synonym: "fractional homology" EXACT [] +synonym: "mixed homology" RELATED [] +synonym: "modular homology" RELATED [] +synonym: "partial correspondence" RELATED [] +synonym: "partial homologous to" EXACT [] +synonym: "percent homology" RELATED [] +synonym: "segmental homology" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000014 +is_symmetric: true +is_a: RO:HOM0000006 ! in structural homology relationship with + +[Typedef] +id: RO:HOM0000015 +name: in protein structural homology relationship with +def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [http://dx.doi.org/10.1016/0022-2836(76)90195-9, http://purl.obolibrary.org/obo/HOM_0000015] +synonym: "protein structural homologous to" EXACT [] +xref: MeSH:Structural_Homology\,_Protein +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000015 +is_symmetric: true +is_a: RO:HOM0000006 ! in structural homology relationship with + +[Typedef] +id: RO:HOM0000016 +name: in non functional homology relationship with +def: "Structural homology that involves a pseudogenic feature and its functional ancestor." [http://purl.obolibrary.org/obo/HOM_0000016, SO:non_functional_homolog_of] +synonym: "non functional homologous to" EXACT [] +synonym: "pseudogene" BROAD [] +xref: SO:non_functional_homolog_of +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000016 +is_symmetric: true +is_a: RO:HOM0000006 ! in structural homology relationship with +disjoint_from: RO:HOM0000062 ! in equivalogy relationship with + +[Typedef] +id: RO:HOM0000017 +name: in orthology relationship with +def: "Historical homology that involves genes that diverged after a speciation event." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000017, http://www.ncbi.nlm.nih.gov/pubmed/5449325] +comment: The term is sometimes also used for anatomical structures. +synonym: "orthologous to" EXACT [] +xref: ECO:00000060 +xref: SO:0000855 +xref: SO:0000858 +xref: SO:orthologous_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000017 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with + +[Typedef] +id: RO:HOM0000018 +name: in xenology relationship with +def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000018] +comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). +synonym: "xenologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000018 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with + +[Typedef] +id: RO:HOM0000019 +name: in 1 to 1 homology relationship with +def: "Historical homology that involves two members sharing no other homologs in the lineages considered." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000019] +synonym: "1 to 1 homologous to" EXACT [] +synonym: "1:1 homology" EXACT [] +synonym: "one-to-one homology" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000019 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with + +[Typedef] +id: RO:HOM0000020 +name: in 1 to 1 orthology relationship with +def: "Orthology that involves two genes that did not experience any duplication after the speciation event that created them." [http://dx.doi.org/10.1007/BF02814484, http://purl.obolibrary.org/obo/HOM_0000020, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "1 to 1 orthologous to" EXACT [] +synonym: "1:1 orthology" EXACT [] +synonym: "one-to-one orthology" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000020 +is_symmetric: true +is_a: RO:HOM0000017 ! in orthology relationship with +is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with + +[Typedef] +id: RO:HOM0000022 +name: in ohnology relationship with +def: "Paralogy that results from a whole genome duplication event." [http://dx.doi.org/10.1038/75560, http://purl.obolibrary.org/obo/HOM_0000022] +synonym: "homoeology" RELATED [] +synonym: "ohnologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000022 +is_symmetric: true +is_a: RO:HOM0000011 ! in paralogy relationship with + +[Typedef] +id: RO:HOM0000023 +name: in in-paralogy relationship with +def: "Paralogy that results from a lineage-specific duplication subsequent to a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000023] +synonym: "in-paralogous to" EXACT [] +synonym: "inparalogy" EXACT [] +synonym: "symparalogy" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000023 +is_symmetric: true +is_a: RO:HOM0000011 ! in paralogy relationship with +disjoint_from: RO:HOM0000024 ! in out-paralogy relationship with + +[Typedef] +id: RO:HOM0000024 +name: in out-paralogy relationship with +def: "Paralogy that results from a duplication preceding a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000024] +synonym: "alloparalogy" EXACT [] +synonym: "out-paralogous to" EXACT [] +synonym: "outparalogy" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000024 +is_symmetric: true +is_a: RO:HOM0000011 ! in paralogy relationship with + +[Typedef] +id: RO:HOM0000025 +name: in pro-orthology relationship with +def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] +synonym: "pro-orthologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000025 +is_symmetric: true +is_a: RO:HOM0000034 ! in 1 to many orthology relationship with + +[Typedef] +id: RO:HOM0000026 +name: in semi-orthology relationship with +def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000026] +comment: The converse of pro-orthologous. +synonym: "semi-orthologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000026 +is_symmetric: true +is_a: RO:HOM0000034 ! in 1 to many orthology relationship with + +[Typedef] +id: RO:HOM0000027 +name: in serial homology relationship with +def: "Iterative homology that involves structures arranged along the main body axis." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000027] +synonym: "homonomy" RELATED [] +synonym: "serial homologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000027 +is_symmetric: true +is_a: RO:HOM0000066 ! in iterative homology relationship with + +[Typedef] +id: RO:HOM0000028 +name: in heterochronous homology relationship with +def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [http://purl.obolibrary.org/obo/HOM_0000028, ISBN:978-0674639416] +synonym: "heterochronous homologous to" EXACT [] +synonym: "heterochrony" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000028 +is_symmetric: true +is_a: RO:HOM0000008 ! in biological homology relationship with + +[Typedef] +id: RO:HOM0000029 +name: in paedomorphorsis relationship with +def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000029, ISBN:978-0674639416] +synonym: "juvenification" EXACT [] +synonym: "pedomorphosis" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000029 +is_symmetric: true +is_a: RO:HOM0000028 ! in heterochronous homology relationship with +disjoint_from: RO:HOM0000030 ! in peramorphosis relationship with + +[Typedef] +id: RO:HOM0000030 +name: in peramorphosis relationship with +def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000030 +is_symmetric: true +is_a: RO:HOM0000028 ! in heterochronous homology relationship with + +[Typedef] +id: RO:HOM0000031 +name: in progenesis relationship with +def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000031 +is_symmetric: true +is_a: RO:HOM0000029 ! in paedomorphorsis relationship with + +[Typedef] +id: RO:HOM0000032 +name: in neoteny relationship with +def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, http://purl.obolibrary.org/obo/HOM_0000032, ISBN:978-0674639416] +synonym: "juvenilization" EXACT [] +synonym: "neotenous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000032 +is_symmetric: true +is_a: RO:HOM0000029 ! in paedomorphorsis relationship with + +[Typedef] +id: RO:HOM0000033 +name: in mimicry relationship with +def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033] +synonym: "mimicrous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000033 +is_symmetric: true +is_a: RO:HOM0000004 ! in convergence relationship with + +[Typedef] +id: RO:HOM0000034 +name: in 1 to many orthology relationship with +def: "Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000034, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "1 to many orthologous to" EXACT [] +synonym: "1:many orthology" EXACT [] +synonym: "co-orthology" RELATED [] +synonym: "many to 1 orthology" RELATED [] +synonym: "one-to-many orthology" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000034 +is_symmetric: true +is_a: RO:HOM0000017 ! in orthology relationship with +is_a: RO:HOM0000037 ! in 1 to many homology relationship with + +[Typedef] +id: RO:HOM0000036 +name: in many to many homology relationship with +def: "Historical homology that involves two members of a larger set of homologs." [http://dx.doi.org/10.1093/molbev/msp002, http://purl.obolibrary.org/obo/HOM_0000036] +synonym: "many to many homologous to" EXACT [] +synonym: "many-to-many homology" EXACT [] +synonym: "many:many homology " EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000036 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with + +[Typedef] +id: RO:HOM0000037 +name: in 1 to many homology relationship with +def: "Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000037] +synonym: "1 to many homologous to" EXACT [] +synonym: "1:many homology" RELATED [] +synonym: "one-to-many homology" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000037 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with + +[Typedef] +id: RO:HOM0000042 +name: in apomorphy relationship with +def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [http://purl.obolibrary.org/obo/HOM_0000042, ISBN:978-0252068140] +synonym: "apomorphous to" EXACT [] +synonym: "synapomorphy" RELATED [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000042 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with +disjoint_from: RO:HOM0000043 ! in plesiomorphy relationship with + +[Typedef] +id: RO:HOM0000043 +name: in plesiomorphy relationship with +def: "Historical homology that is based on distant shared ancestry." [http://purl.obolibrary.org/obo/HOM_0000043, ISBN:978-0252068140] +comment: This term is usually contrasted to apomorphy. +synonym: "plesiomorphous to" EXACT [] +synonym: "symplesiomorphy" RELATED [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000043 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with + +[Typedef] +id: RO:HOM0000044 +name: in deep homology relationship with +def: "Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1038/nature07891, http://purl.obolibrary.org/obo/HOM_0000044] +comment: Used for structures in distantly related taxa. +synonym: "deep genetic homology" EXACT [] +synonym: "deep homologous to" EXACT [] +synonym: "generative homology" RELATED [] +synonym: "homoiology" RELATED [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000044 +is_symmetric: true +is_a: RO:HOM0000003 ! in homocracy relationship with +is_a: RO:HOM0000005 ! in parallelism relationship with + +[Typedef] +id: RO:HOM0000045 +name: in hemiplasy relationship with +def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] +synonym: "hemiplasous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000045 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with + +[Typedef] +id: RO:HOM0000046 +name: in gametology relationship with +def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] +synonym: "gametologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000046 +is_symmetric: true +is_a: RO:HOM0000047 ! in chromosomal homology relationship with + +[Typedef] +id: RO:HOM0000047 +name: in chromosomal homology relationship with +def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [http://purl.obolibrary.org/obo/HOM_0000047, ISBN:0195307615] +synonym: "chromosomal homologous to" EXACT [] +xref: MeSH:Chromosome_Pairing +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000047 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with + +[Typedef] +id: RO:HOM0000048 +name: in many to many orthology relationship with +def: "Orthology that involves two genes that experienced duplications more recent than the species split that created them." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000048, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "co-orthology" RELATED [] +synonym: "many to many orthologous to" EXACT [] +synonym: "many-to-many orthology" EXACT [] +synonym: "many:many orthology" EXACT [] +synonym: "trans-homology" RELATED [] +synonym: "trans-orthology" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000048 +is_symmetric: true +is_a: RO:HOM0000017 ! in orthology relationship with +is_a: RO:HOM0000036 ! in many to many homology relationship with + +[Typedef] +id: RO:HOM0000049 +name: in within-species paralogy relationship with +def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "within-species paralogous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000049 +is_symmetric: true +is_a: RO:HOM0000011 ! in paralogy relationship with +disjoint_from: RO:HOM0000050 ! in between-species paralogy relationship with + +[Typedef] +id: RO:HOM0000050 +name: in between-species paralogy relationship with +def: "Paralogy that involves genes from different species." [http://purl.obolibrary.org/obo/HOM_0000050, http://www.ensembl.org/info/docs/compara/homology_method.html] +comment: The genes have diverged before a speciation event. +synonym: "between-species paralogous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000050 +is_symmetric: true +is_a: RO:HOM0000011 ! in paralogy relationship with + +[Typedef] +id: RO:HOM0000051 +name: in postdisplacement relationship with +def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] +synonym: "post-displacement" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000051 +is_symmetric: true +is_a: RO:HOM0000029 ! in paedomorphorsis relationship with + +[Typedef] +id: RO:HOM0000052 +name: in hypermorphosis relationship with +def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000052 +is_symmetric: true +is_a: RO:HOM0000030 ! in peramorphosis relationship with + +[Typedef] +id: RO:HOM0000053 +name: in synology relationship with +def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] +synonym: "synologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000053 +is_symmetric: true +is_a: RO:HOM0000018 ! in xenology relationship with + +[Typedef] +id: RO:HOM0000054 +name: in isoorthology relationship with +def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000054] +synonym: "isoorthologous to" EXACT [] +xref: ECO:0000080 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000054 +is_symmetric: true +is_a: RO:HOM0000017 ! in orthology relationship with +is_a: RO:HOM0000062 ! in equivalogy relationship with + +[Typedef] +id: RO:HOM0000055 +name: in tandem paralogy relationship with +def: "Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000055, ISBN:978-0878932665] +synonym: "iterative paralogy" RELATED [] +synonym: "serial paralogy" RELATED [] +synonym: "tandem paralogous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000055 +is_symmetric: true +is_a: RO:HOM0000011 ! in paralogy relationship with + +[Typedef] +id: RO:HOM0000057 +name: in latent homology relationship with +def: "Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character)." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000057, ISBN:0199141118] +comment: Used for structures in closely related taxa. +synonym: "apomorphic tendency" EXACT [] +synonym: "cryptic homology" EXACT [] +synonym: "homoiology" RELATED [] +synonym: "homoplastic tendency" RELATED [] +synonym: "latent homologous to" EXACT [] +synonym: "re-awakening" RELATED [] +synonym: "underlying synapomorphy" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000057 +is_symmetric: true +is_a: RO:HOM0000005 ! in parallelism relationship with +is_a: RO:HOM0000058 ! in syngeny relationship with + +[Typedef] +id: RO:HOM0000058 +name: in syngeny relationship with +def: "Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual." [DOI:10.1002/1521-1878(200009)22\:9<846\:\:AID-BIES10>3.0.CO;2-R, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000058] +comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. +synonym: "generative homology" EXACT [] +synonym: "syngenous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000058 +is_symmetric: true +is_a: RO:HOM0000003 ! in homocracy relationship with + +[Typedef] +id: RO:HOM0000060 +name: in apparent orthology relationship with +def: "Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000060, http://www.ensembl.org/info/docs/compara/homology_method.html] +comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. +synonym: "1:1 paralogy" EXACT [] +synonym: "apparent 1:1 orthology" EXACT [] +synonym: "apparent orthologous to" EXACT [] +synonym: "pseudoorthology" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000060 +is_symmetric: true +is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with +is_a: RO:HOM0000050 ! in between-species paralogy relationship with + +[Typedef] +id: RO:HOM0000061 +name: in pseudoparalogy relationship with +def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000061] +comment: These genes may come out as paralogs in a single-genome analysis. +synonym: "pseudoparalogous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000061 +is_symmetric: true +is_a: RO:HOM0000018 ! in xenology relationship with + +[Typedef] +id: RO:HOM0000062 +name: in equivalogy relationship with +def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1093/nar/gkl1043, http://purl.obolibrary.org/obo/HOM_0000062] +comment: This may include examples of orthology, paralogy and xenology. +synonym: "equivalogous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000062 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with +is_a: RO:HOM0000065 ! in functional equivalence relationship with + +[Typedef] +id: RO:HOM0000063 +name: in interology relationship with +def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] +synonym: "interologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000063 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with + +[Typedef] +id: RO:HOM0000065 +name: in functional equivalence relationship with +def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] +synonym: "functional similarity" RELATED [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000065 +is_symmetric: true +is_a: RO:HOM0000000 ! in similarity relationship with + +[Typedef] +id: RO:HOM0000066 +name: in iterative homology relationship with +def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] +synonym: "iterative homologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000066 +is_symmetric: true +is_a: RO:HOM0000008 ! in biological homology relationship with + +[Typedef] +id: RO:HOM0000068 +name: in paraxenology relationship with +def: "Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome." [http://purl.obolibrary.org/obo/HOM_0000068, http://www.ncbi.nlm.nih.gov/pubmed/3065587] +synonym: "duplicate xenology" EXACT [] +synonym: "multiple xenology" EXACT [] +synonym: "paraxenologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000068 +is_symmetric: true +is_a: RO:HOM0000018 ! in xenology relationship with + +[Typedef] +id: RO:HOM0000069 +name: in plerology relationship with +def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [http://purl.obolibrary.org/obo/HOM_0000069, http://www.ncbi.nlm.nih.gov/pubmed/3065587] +comment: This phenomenon is usually due to gene conversion process. +synonym: "plerologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000069 +is_symmetric: true +is_a: RO:HOM0000011 ! in paralogy relationship with + +[Typedef] +id: RO:HOM0000071 +name: in homotopy relationship with +def: "Structural homology that involves structures with the same or similar relative positions." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/BF02814485, http://purl.obolibrary.org/obo/HOM_0000071, ISBN:0123195837] +comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. +synonym: "homotopous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000071 +is_symmetric: true +is_a: RO:HOM0000006 ! in structural homology relationship with +disjoint_from: RO:HOM0000072 ! in homeosis relationship with + +[Typedef] +id: RO:HOM0000072 +name: in homeosis relationship with +def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] +synonym: "heterotopy" RELATED [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000072 +is_symmetric: true +is_a: RO:HOM0000008 ! in biological homology relationship with + +[Typedef] +id: RO:HOM0000073 +name: in homoeology relationship with +def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pnas.0505156102, http://purl.obolibrary.org/obo/HOM_0000073] +comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. +synonym: "homoeologous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000073 +is_symmetric: true +is_a: RO:HOM0000022 ! in ohnology relationship with +is_a: RO:HOM0000053 ! in synology relationship with + +[Typedef] +id: RO:HOM0000074 +name: in paramorphism relationship with +def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] +synonym: "axis paramorphism" RELATED [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000074 +is_symmetric: true +is_a: RO:HOM0000003 ! in homocracy relationship with +is_a: RO:HOM0000066 ! in iterative homology relationship with + +[Typedef] +id: RO:HOM0000075 +name: in regulogy relationship with +def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] +synonym: "regulogous to" EXACT [] +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000075 +is_symmetric: true +is_a: RO:HOM0000007 ! in historical homology relationship with + diff --git a/ro-full.owl b/ro-full.owl new file mode 100644 index 00000000..83a9affa --- /dev/null +++ b/ro-full.owl @@ -0,0 +1,15242 @@ + + + + + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. + OBO Relations Ontology + + 2023-02-19 + https://github.com/oborel/obo-relations/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + + + + + + + + + + OBO foundry unique label + + + + + + + + + + + + + + + + + + + + + term replaced by + + + + + + + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + defined by construct + + + + + + + + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + temporal interpretation + + + + + + + + + + tooth SubClassOf 'never in taxon' value 'Aves' + x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. + + + + Class: ?X DisjointWith: RO_0002162 some ?Y + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> +PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> +CONSTRUCT { + in_taxon: a owl:ObjectProperty . + ?x owl:disjointWith [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom ?taxon + ] . + ?x rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom [ + a owl:Class ; + owl:complementOf ?taxon + ] + ] . +} +WHERE { + ?x never_in_taxon: ?taxon . +} + never in taxon + + + + + + + + + + A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. + non-overlapping with + shares no parts with + + Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) + PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> +PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> +CONSTRUCT { + part_of: a owl:ObjectProperty . + [ + a owl:Restriction ; + owl:onProperty part_of: ; + owl:someValuesFrom ?x ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty part_of: ; + owl:someValuesFrom ?y + ] + ] +} +WHERE { + ?x mutually_spatially_disjoint_with: ?y . +} + mutually spatially disjoint with + + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + + + + + + + + + An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. + taxonomic class assertion + + + + + + + + + + S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] + ambiguous for taxon + + + + + + + + + + S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. + + + This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost + dubious for taxon + + + + + + + + + + S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S + + + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> +PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> +CONSTRUCT { + in_taxon: a owl:ObjectProperty . + ?witness rdfs:label ?label . + ?witness rdfs:subClassOf ?x . + ?witness rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom ?taxon + ] . +} +WHERE { + ?x present_in_taxon: ?taxon . + BIND(IRI(CONCAT( + "http://purl.obolibrary.org/obo/RO_0002175#", + MD5(STR(?x)), + "-", + MD5(STR(?taxon)) + )) as ?witness) + BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) +} + The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. + present in taxon + + + + + + + + + + defined by inverse + + + + + + + + + An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. + logical macro assertion + http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ + + + + + + + + An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. + annotation property cardinality + + + + + + + + + + A logical macro assertion whose domain is an IRI for a class + The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL + logical macro assertion on a class + + + + + + + + + A logical macro assertion whose domain is an IRI for a property + logical macro assertion on a property + + + + + + + + + Used to annotate object properties to describe a logical meta-property or characteristic of the object property. + logical macro assertion on an object property + + + + + + + + + logical macro assertion on an annotation property + + + + + + + + + An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. + dispositional interpretation + + + + + + + + + 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' + A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. + shares no connection with + Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) + has no connections with + + + + + + + + + inherited annotation property + + + + + + + + Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) + curator guidance link + + + + + + + + + brain always_present_in_taxon 'Vertebrata' + forelimb always_present_in_taxon Euarchontoglires + S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S + This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. + never lost in + always present in taxon + + + + + + + + + This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. + temporal logical macro assertion on a class + + + + + + + + + measurement property has unit + + + + + + + + + has start time value + + + + + + + + + + has end time value + + + + + + + + + + Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. + start, days post fertilization + + + + + + + + + + Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. + end, days post fertilization + + + + + + + + + + Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. + start, years post birth + + + + + + + + + + Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 + end, years post birth + + + + + + + + + + Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. + start, months post birth + + + + + + + + + + Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 + end, months post birth + + + + + + + + + + Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. + month of gestation + + + + + + + + + + A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process + has developmental stage marker + + + + + + + + + + Count of number of days intervening between the start of the stage and the time of coitum. + For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) + start, days post coitum + + + + + + + + + + Count of number of days intervening between the end of the stage and the time of coitum. + end, days post coitum + + + + + + + + + + start, weeks post birth + + + + + + + + + + end, weeks post birth + + + + + + + + + + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p + is asymmetric relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p + is symmetric relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process + is relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y + The general property hierarchy is: + + "directly P" SubPropertyOf "P" + Transitive(P) + +Where we have an annotation assertion + + "directly P" "is direct form of" "P" + If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' + + is direct form of + + + + + + + + + + relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y + + is indirect form of + + + + + + + + + + logical macro assertion on an axiom + + + + + + + + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom + + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. + is relational form of a class + + + + + + + + + A shortcut relationship that holds between two entities based on their identity criteria + logical macro assertion involving identity + + + + + + + + + A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. + in approximate one to one relationship with + + + + + + + + + x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y + The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" + is approximately equivalent to + + + + + + + + + 'anterior end of organism' is-opposite-of 'posterior end of organism' + 'increase in temperature' is-opposite-of 'decrease in temperature' + x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + is opposite of + + + + + + + + + x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + is indistinguishable from + + + + + + + + + evidential logical macro assertion on an axiom + + + + + + + + + A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom has evidence + + + + + + + + + A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom contradicted by evidence + + + + + + + + + In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. + this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. + If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion + is representative IRI for equivalence set + OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member + + + + + + + + + true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. + + nominally disjoint with + + + + + + + + + Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" + + 2018-03-13T23:59:29Z + is directional form of + + + + + + + + + + 2018-03-14T00:03:16Z + is positive form of + + + + + + + + + + 2018-03-14T00:03:24Z + is negative form of + + + + + + + + + part-of is homeomorphic for independent continuants. + R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. + + 2018-10-21T19:46:34Z + R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. + is homeomorphic for + + + + + + + + + + pg + 2020-09-22T11:05:29Z + valid_for_go_annotation_extension + + + + + + + + + + pg + 2020-09-22T11:05:18Z + valid_for_go_gp2term + + + + + + + + + + pg + 2020-09-22T11:04:12Z + valid_for_go_ontology + + + + + + + + + + pg + 2020-09-22T11:05:45Z + valid_for_gocam + + + + + + + + + + eco subset + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subset_property + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_broad_synonym + + + + + + + + database_cross_reference + + + + + + + + has_exact_synonym + + + + + + + + has_narrow_synonym + + + + + + + + has_obo_format_version + + + + + + + + has_related_synonym + + + + + + + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + is defined by + + + + + is defined by + This is an experimental annotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + + + + + + + + + + + + part of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + + + + has part + + + + + + + + + + + realized in + this disease is realized in this disease course + this fragility is realized in this shattering + this investigator role is realized in this investigation + is realized by + realized_in + [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + + + realizes + this disease course realizes this disease + this investigation realizes this investigator role + this shattering realizes this fragility + to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + accidentally included in BFO 1.2 proposal + - should have been BFO_0000062 + obsolete preceded by + true + + + + + + + + + + + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by + + + + + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + + + + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in + + + + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity. + derives from part of + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + has characteristic + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + + + + + + + OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete in neural circuit with + true + + + + + + + + + + OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete upstream in neural circuit with + true + + + + + + + + + + OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete downstream in neural circuit with + true + + + + + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + + derives from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + + derives into + + + + + + + + + + is location of + my head is the location of my brain + this cage is the location of this rat + a relation between two independent continuants, the location and the target, in which the target is entirely within the location + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + location_of + + location of + + + + + + + + + + + + + + + contained in + Containment is location not involving parthood, and arises only where some immaterial continuant is involved. + Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): + Intended meaning: +domain: material entity +range: spatial region or site (immaterial continuant) + + contained_in + + + contained in + + + + + + + + contains + + + contains + + + + + + + + + + + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is allergic trigger for + + + + + + + + + + + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is autoimmune trigger for + + + + + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has allergic trigger + + + + + + + + + + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has autoimmune trigger + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in + + located in + + + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. + + + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. + + + + + + + + + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of + surface of + + 2D boundary of + + + + + + + + + + May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 + + + aligned with + + + + + + + + + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + + has boundary + has_2D_boundary + + has 2D boundary + + + + + + + + + A relation that holds between two neurons that are electrically coupled via gap junctions. + + + electrically_synapsed_to + + + + + + + + + + + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + + tracheates + + + + + + + + + + + + http://www.ncbi.nlm.nih.gov/pubmed/22402613 + innervated_by + + + + + + + + + + + + has synaptic terminal of + + + + + + + + + + + + + + + + + + + + + X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. + bounding layer of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + Note from NCEAS meeting: consider changing primary label + + + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. + coincident with + + + + + + + + + + A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. + + x 'cell expresses' y iff: +cell(x) +AND gene(y) +AND exists some 'transcription, DNA templated (GO_0006351)'(t) +AND t occurs_in x +AND t has_input y + cell expresses + + + + + + + + + + + x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + regulates in other organism + + + + + + + + + + + + A relationship that holds between a process that regulates a transport process and the entity transported by that process. + + + regulates transport of + + + + + + + + + + + + A part of relation that applies only between occurrents. + occurrent part of + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + dos + 2017-07-19T17:30:36Z + has ligand + + + + + + + + + Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. + dos + 2017-07-20T17:11:08Z + transports + + + + + + + + + A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. + dos + 2017-07-20T17:19:37Z + occurs across + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + + + A relationship that holds between two images, A and B, where: +A depicts X; +B depicts Y; +X and Y are both of type T' +C is a 2 layer image consiting of layers A and B; +A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. +Note: A and B may be 2D or 3D. +Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. + dos + 2017-12-07T12:58:06Z + in register with + + + + + A relationship that holds between two images, A and B, where: +A depicts X; +B depicts Y; +X and Y are both of type T' +C is a 2 layer image consiting of layers A and B; +A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. +Note: A and B may be 2D or 3D. +Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. + GOC:dos + + + + + + + + + David Osumi-Sutherland + <= + + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + + + + + David Osumi-Sutherland + + starts before + + + + + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + + + + + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + + + + + + + + + + + + + + + + Relation between a neuron and an anatomical structure that its soma is part of. + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) + + has soma location + + + + + + + + + + + + + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. + + + fasciculates with + (forall (?x ?y) + (iff + (fasciculates_with ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron ; CL_0000540" ?x) + ("neuron projection bundle ; CARO_0001001" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500' " ?npbs) + (part_of ?npbs ?y) + (part_of ?nps ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + + fasciculates with + + + + + + + + + + + + + + + Relation between a neuron and some structure its axon forms (chemical) synapses in. + + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( + <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) + + + axon synapses in + + + + + + + + + + + + + + + + + + + + + + Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + synapsed by + + + + + + + + + + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] + + Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. + + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) + + has plasma membrane part + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. + + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_Ib_bouton_to + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. + + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_Is_bouton_to + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type II bouton. + + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_II_bouton_to + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type II bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_II_bouton + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_Ib_bouton + + + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + + + synapsed in + http://purl.obolibrary.org/obo/BFO_0000051 some ( + http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( + http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) + + + has postsynaptic terminal in + + + + + + + + + + + has neurotransmitter + releases neurotransmitter + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_Is_bouton + + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + synapses in + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) + + + has presynaptic terminal in + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type III bouton. + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_III_bouton_to + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type III bouton. + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_III_bouton + + + + + + + + + + + + + + + + + + + + + Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + N1 synapsed_to some N2 +Expands to: +N1 SubclassOf ( + has_part some ( + ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( + ‘synapse ; GO:0045202’ that has_part some ( + ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) + synapsed to + + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. + + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( + http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( + <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) + + + dendrite synapsed in + + + + + + + + + + + + + + + A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. + + has synapse in + <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) + + + has synaptic terminal in + + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + + + overlaps + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + + The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. + + has fasciculating component + (forall (?x ?y) + (iff + (has_fasciculating_neuron_projection ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron projection bundle ; CARO_0001001" ?x) + ("neuron projection ; GO0043005" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500" ?npbs) + (part_of ?nps ?y) + (part_of ?npbs ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + + + + + has fasciculating neuron projection + + + + + + + + + + + + + + Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. +T innervates some R +Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + innervates + + + + + + + + + + + + + X continuous_with Y if and only if X and Y share a fiat boundary. + + connected to + The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) + + continuous with + FMA:85972 + + + + + + + + + + x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x + We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom + proper overlaps + (forall (?x ?y) + (iff + (proper_overlaps ?x ?y) + (and + (overlaps ?x ?y) + (not (part_of ?x ?y)) + (not (part_of ?y ?x))))) + + + partially overlaps + + + + + + + + + + + + d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + ancestral_stucture_of + evolutionarily_descended_from + derived by descent from + + + + + + + + + + + inverse of derived by descent from + + has derived by descendant + + + + + + + + + + + + + + + + two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + Consider obsoleting and merging with child relation, 'in homology relationship with' + VBO calls this homologous_to + shares ancestor with + + + + + + + + + + + + serially homologous to + + + + + + + + + lactation SubClassOf 'only in taxon' some 'Mammalia' + + x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. + + 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria + + + + only in taxon + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + + + + + + Connects a biological entity to its taxon of origin. + in taxon + + + + + + + + + + + A is spatially_disjoint_from B if and only if they have no parts in common + There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. + + + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy + BFO_0000051 exactly 0 (BFO_0000050 some ?Y) + + + spatially disjoint from + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + + + + + + + + + + + + + + + + + + + + + + + + + + + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b + + connected to + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + + + + + + + + + + + + + + + + The M8 connects Glasgow and Edinburgh + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. + + connects + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + + + + + + + + + + + + + + + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) + attached to part of + + + + + + + + + true + + + + + + + + + Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. + Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure + + supplies + + + + + + + + + Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. + Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure + + drains + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component + + + + + + + + + + + + + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + + + has phenotype + + + + + + + + + + inverse of has phenotype + + + + phenotype of + + + + + + + + + + + + + + x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + + + + + This is the transitive form of the develops from relation + develops from + + + + + + + + + + + + + inverse of develops from + + + + + develops into + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" + We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. + + gene product of + + + + + + + + + + + + + + + every HOTAIR lncRNA is the gene product of some HOXC gene + every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene + + x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y + + has gene product + + + + + + + + + + + + + + + + + + + + + + + + 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' + + x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process + + expressed in + + + + + + + + + + + + + + + + + + + + + + + + + + + Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. + + + FBbt + + has developmental precursor + TODO - add child relations from DOS + directly develops from + + + + + + + + + + A parasite that kills or sterilizes its host + parasitoid of + + + + + + + + + inverse of parasitoid of + + has parasitoid + + + + + + + + + + inverse of directly develops from + developmental precursor of + + directly develops into + + + + + + + + + + + + + + + + + + + + + + + + + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. + + + + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + + + + regulates + + + + + + + + + + + + + + + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. + + + negatively regulates (process to process) + + + + + negatively regulates + + + + + + + + + + + + + + + + + + + + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. + + + positively regulates (process to process) + + + + + positively regulates + + + + + + + + + + + + + + + + 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) + heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') + + x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. + Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + TODO: add homeomorphy axiom + This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. + + has prototype + + + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + + capable of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + + has function in + capable of part of + + + + + + + + + + true + + + + + + + + OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role + + agent in + + Obsoleted as the inverse property was obsoleted. + obsolete actively participates in + true + + + + + + + + OBSOLETE x has participant y if and only if x realizes some active role that inheres in y + + has agent + + obsolete has active participant + true + + + + + + + + + + + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x + + + surrounded by + + + + + + + + + + + A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. + The epidermis layer of a vertebrate is adjacent to the dermis. + The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. + The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. + + x adjacent to y if and only if x and y share a boundary. + This relation acts as a join point with BSPO + + + + + + adjacent to + + + + + A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. + + + + + + + + + + + inverse of surrounded by + + + + surrounds + + + + + + + + + + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + inverse of starts with + + Chris Mungall + Allen + + starts + + + + + + + + + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + started by + + starts with + + + + + + + + + + + + + + x develops from part of y if and only if there exists some z such that x develops from z and z is part of y + + develops from part of + + + + + + + + + + + + + + + x develops_in y if x is located in y whilst x is developing + + EHDAA2 + Jonathan Bard, EHDAA2 + develops in + + + + + + + + + A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. + obligate parasite of + + + + + + + + + A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. + facultative parasite of + + + + + + + + + + + + inverse of ends with + + Chris Mungall + + ends + + + + + + + + + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + finished by + + ends with + + + + + + + + + + + + + + + + x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + + starts with process that occurs in + + has start location + + + + + + + + + + + + + + + + x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + + ends with process that occurs in + + has end location + + + + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + consumes + + + + + has input + + + + + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + + produces + + + + + has output + + + + + + + + + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) + stem parasite of + + + + + + + + + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) + root parasite of + + + + + + + + + A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. + hemiparasite of + + + + + + + + + X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. + + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). + +If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + has component participant + + + + + + + + + A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. + ExO:0000001 + has exposure receptor + + + + + + + + + A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. + ExO:0000000 + has exposure stressor + + + + + + + + + A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor + ExO:0000055 + has exposure route + + + + + + + + + A broad relationship between an exposure event or process and the course takes from the source to the target. + http://purl.obolibrary.org/obo/ExO_0000004 + has exposure transport path + + + + + + + + + + Any relationship between an exposure event or process and any other entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. + related via exposure to + + + + + + + + + g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. + over-expressed in + + + + + + + + + g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. + under-expressed in + + + + + + + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. + has active substance + has active pharmaceutical ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + + active ingredient in + + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. + b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. + + connecting branch of + + + + + + + + + + inverse of connecting branch of + + + has connecting branch + + + + + + + + + + + + + + + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] + + x has developmental contribution from y iff x has some part z such that z develops from y + + has developmental contribution from + + + + + + + + + + + + + + + inverse of has developmental contribution from + + + developmentally contributes to + + + + + + + + + + + + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T + + + + induced by + + Developmental Biology, Gilbert, 8th edition, figure 6.5(F) + GO:0001759 + We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] + developmentally induced by + + + + + + + + + + + Inverse of developmentally induced by + + developmentally induces + + + + + + + + + + + + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + false + + In general you should not use this relation to make assertions - use one of the more specific relations below this one + This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from + developmentally preceded by + + + + + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + has chemical role + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + + acts upstream of or within + + + + + + + + + + + x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else + This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage + + replaces + developmentally replaces + + + + + + + + + + Inverse of developmentally preceded by + + developmentally succeeded by + + + + + + + + + + + + + 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue + + + part of developmental precursor of + + + + + + + + + + + x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x + Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. + + ubiquitously expressed in + + + + + + + + + + Inverse of 'expressed in' + + expresses + + + + + + + + + + inverse of ubiquiotously expressed in + + + ubiquitously expresses + + + + + + + + + + + + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). + This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. + + results in developmental progression of + + + + + + + + + + + every flower development (GO:0009908) results in development of some flower (PO:0009046) + + p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. + + http://www.geneontology.org/GO.doc.development.shtml + + + + results in development of + + + + + + + + + + + an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. + every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + + + GOC:mtg_berkeley_2013 + + + + results in formation of + + + + + + + + + + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. + tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) + + The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. + + GOC:mtg_berkeley_2013 + + + + results in morphogenesis of + + + + + + + + + + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process + bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) + + The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + + GOC:mtg_berkeley_2013 + + + + results in maturation of + + + + + + + + + foramen ovale closure SubClassOf results in disappearance of foramen ovale + + + May be merged into parent relation + results in disappearance of + + + + + + + + + every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) + + + May be merged into parent relation + results in developmental regression of + + + + + + + + + + Inverse of 'is substance that treats' + + + is treated by substance + + + + + + + + + + + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' +where +'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview + + x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. + + adapted for living in + + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. + has habitat + + + + + + + + + + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. + + + + + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. + + + + + causally upstream of, negative effect + + + + + + + + + A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. + + + + + 2017-06-05T17:35:04Z + has exposure stimulus + + + + + + + + + + evolutionary variant of + + + + + + + + + + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. + + regulates localization of + + + + transports or maintains localization of + + + + + + + + + + + + + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + characteristic of part of + + + + + + + + + + true + + + + + + + + + + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. + The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity + + GOC:mtg_berkeley_2013 + + + + results in acquisition of features of + + + + + + + + A relationship that holds via some environmental process + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + evolutionarily related to + + + + + + + + A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + + ecologically related to + + + + + + + + + + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. + + adapted for + + confers advantage in + + + + + + + + A mereological relationship or a topological relationship + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to + + + + + + + + A relationship that holds between entities participating in some developmental process (GO:0032502) + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development + developmentally related to + + + + + + + + + + + Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) + a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. + + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] + + colocalizes with + + + + + + + + + + ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. + Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. + eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex + We would like to say + +if and only if + exists c', p' + c part_of c' and c' capable_of p + and + c capable_of p' and p' part_of p +then + c contributes_to p + +However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. + + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + + contributes to + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. + + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + + This is a grouping relation that collects relations used for the purpose of connecting structure and function + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + + false + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism + genomically related to + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + + actively involved in + enables part of + involved in + + + + + + + + + + + + every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid + p regulates levels of c if p regulates some amount (PATO:0000070) of c + + + regulates levels of (process to entity) + regulates levels of + + + + + + + + + + inverse of enables + + + enabled by + + + + + + + + + + + + inverse of regulates + + regulated by (processual) + + regulated by + + + + + + + + + inverse of negatively regulates + + + negatively regulated by + + + + + + + + + inverse of positively regulates + + + positively regulated by + + + + + + + + + + A relationship that holds via some process of localization + + Do not use this relation directly. It is a grouping relation. + related via localization to + + + + + + + + + + + + + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. + + + + + has target start location + + + + + + + + + + + + + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. + + + + + has target end location + + + + + + + + + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. + + + imports + + + + + + + + + Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l + + results in transport along + + + + + + + + + + Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. + + + results in transport across + + + + + + + + + + 'pollen tube growth' results_in growth_of some 'pollen tube' + + results in growth of + + + + + + + + + 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) + + results in transport to from or in + + + + + + + + + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + + + exports + + + + + + + + + + an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. + p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. + + + + + results in commitment to + + + + + + + + + + p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. + + + + + results in determination of + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + inverse of has input + + + + input of + + + + + + + + + + inverse of has output + + + + output of + + + + + + + + + + formed as result of + + + + + + + + + + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. + + results in structural organization of + + + + + + + + + + The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. + + + + + results in specification of + + + + + + + + + p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. + + results in developmental induction of + + + + + + + + + + http://neurolex.org/wiki/Property:DendriteLocation + has dendrite location + + + + + + + + + + + a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a + + attached to (anatomical structure to anatomical structure) + + attached to + + + + + + + + + + + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. + + Wikipedia:Insertion_(anatomy) + has muscle origin + + + + + + + We need to import uberon muscle to create a stricter domain constraint + + + + + + + + + + + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + + Wikipedia:Insertion_(anatomy) + has muscle insertion + + + + + + + We need to import uberon muscle into RO to use as a stricter domain constraint + + + + + + + + + false + + x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat + + + has fused element + A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. + derived from ancestral fusion of + + + + + + + + + + + + A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) + + in branching relationship with + + https://github.com/obophenotype/uberon/issues/170 + + + + + + + + + + Deschutes River tributary_of Columbia River + inferior epigastric vein tributary_of external iliac vein + + x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. + + drains into + drains to + tributary channel of + http://en.wikipedia.org/wiki/Tributary + http://www.medindia.net/glossary/venous_tributary.htm + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) + + tributary of + + http://en.wikipedia.org/wiki/Tributary + + + + + + + + + + Deschutes River distributary_of Little Lava Lake + + x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x + + branch of + distributary channel of + http://en.wikipedia.org/wiki/Distributary + + This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes + distributary of + + + + + + + + + + + + + + + + + x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. + + anastomoses with + + anabranch of + + + + + + + + + + + + + + + A lump of clay and a statue + x spatially_coextensive_with y if and inly if x and y have the same location + + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios + spatially coextensive with + + + + + + + + + + + + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S + x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y + + + branching part of + + FMA:85994 + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. + + x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. + + + main stem of + + + + + + + + + + + x proper_distributary_of y iff x distributary_of y and x does not flow back into y + + + proper distributary of + + + + + + + + + + x proper_tributary_of y iff x tributary_of y and x does not originate from y + + + proper tributary of + + + + + + + + + + + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + + has developmental potential involving + + + + + + + + + + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + + has potential to developmentally contribute to + + + + + + + + + + x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y + + has potential to developmentally induce + + + + + + + + + + x has the potential to develop into y iff x develops into y or if x is capable of developing into y + + has potential to develop into + + + + + + + + + + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + + has potential to directly develop into + + + + + + + + + + + + + 'protein catabolic process' SubClassOf has_direct_input some protein + + p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + directly consumes + This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' + has direct input + + + + + + + + + + Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + obsolete has indirect input + true + + + + + + + + translation SubClassOf has_direct_output some protein + + p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. + + directly produces + obsolete has direct output + true + + + + + + + + + + + + + + Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + obsolete has indirect output + true + + + + + + + + + + + + inverse of upstream of + + causally downstream of + + + + + + + + + + + + + immediately causally downstream of + + + + + + + + + This term was obsoleted because it has the same meaning as 'directly positively regulates'. + obsolete directly activates + true + + + + + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + + indirectly activates + + indirectly positively regulates + + + + + + + + + This term was obsoleted because it has the same meaning as 'directly negatively regulates'. + obsolete directly inhibits + true + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + + indirectly inhibits + + indirectly negatively regulates + + + + + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative? + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types. + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causally related to + + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + + + + + + + + + + + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. + + + + causally upstream of + + + + + + + + + + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. + + + immediately causally upstream of + + + + + + + + + + + + + + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. + This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit + + directly provides input for + + directly provides input for (process to process) + provides input for + + + + + + + + + + + + + transitive form of directly_provides_input_for + + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. + transitively provides input for (process to process) + transitively provides input for + + + + + + + + + + + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + + influences (processual) + affects + causally upstream of or within + + + + + + + + false + + This is an exploratory relation + differs in + https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions + + + + + + + + + + + + + + + + + + differs in attribute of + + + + + + + + + + + differs in attribute + + + + + + + + + + inverse of causally upstream of or within + + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + + + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union + + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + + + + A protein that enables activity in a cytosol. + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + + executes activity in + enables activity in + + is active in + + + + + + + + + true + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + + + + + + + + + p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. + + contributes to morphology of + + + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Considering relabeling as 'pairwise interacts with' + + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 + + + + + + + + + + An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) + + genetically interacts with + + http://purl.obolibrary.org/obo/MI_0208 + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + + + + + An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. + + interacts with on organism level + + biotically interacts with + + http://eol.org/schema/terms/interactsWith + + + + + + + + + An interaction relationship in which the partners are related via a feeding relationship. + + + trophically interacts with + + + + + + + + + + + A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] + Baleen whale preys on krill + An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members + + + + is subject of predation interaction with + preys upon + + preys on + http://eol.org/schema/terms/preysUpon + http://www.inaturalist.org/observations/2942824 + + + + + + + + + + + + + + + + + A biotic interaction in which the two organisms live together in more or less intimate association. + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism + + symbiotically interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + + commensually interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + + mutualistically interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + This relation groups a pair of inverse relations, parasite of and parasitized by + + interacts with via parasite-host interaction + + + + + + + + + + + + + + + + + + Pediculus humanus capitis parasite of human + + parasitizes + direct parasite of + + parasite of + http://eol.org/schema/terms/parasitizes + + + + + + + + + + + has parasite + parasitised by + directly parasitized by + + parasitized by + http://eol.org/schema/terms/hasParasite + + + + + + + + + Porifiera attaches to substrate + A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. + + semibiotically interacts with + + participates in a abiotic-biotic interaction with + + + + + + + + + + + + + + + Axiomatization to GO to be added later + + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + phosphorylates + + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. + + + molecularly controls + directly regulates activity of + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + + + directly inhibits + molecularly decreases activity of + directly negatively regulates activity of + + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + + + directly activates + molecularly increases activity of + directly positively regulates activity of + + + + + + + + + all dengue disease transmitted by some mosquito + A relationship that holds between a disease and organism + Add domain and range constraints + + transmitted by + + + + + + + + + + A relation that holds between a disease or an organism and a phenotype + + has symptom + + + + + + + + + + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) + + host of + + + + + + + + + X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y + + + has host + http://eol.org/schema/terms/hasHost + + + + + + + + + + Bees pollinate Flowers + This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. + + is subject of pollination interaction with + + pollinates + http://eol.org/schema/terms/pollinates + + + + + + + + + + has polinator + is target of pollination interaction with + + pollinated by + http://eol.org/schema/terms/hasPollinator + + + + + + + + + + + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. + + acquires nutrients from + + + + + + + + + inverse of preys on + + has predator + is target of predation interaction with + + + preyed upon by + http://eol.org/schema/terms/HasPredator + http://polytraits.lifewatchgreece.eu/terms/PRED + + + + + + + + + + Anopheles is a vector for Plasmodium + + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism + + is vector for + + + + + + + + + + + has vector + + + + + + + + + + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + partner in + + + + + + + + + + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + subject participant in + + + + + + + + + + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. + target participant in + + + + + + + + + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + helper property (not for use in curation) + + + + + + + + + + is symbiosis + + + + + + + + + + is commensalism + + + + + + + + + + is mutualism + + + + + + + + + + is parasitism + + + + + + + + + + + provides nutrients for + + + + + + + + + + is subject of eating interaction with + + eats + + + + + + + + + + eaten by + is target of eating interaction with + + is eaten by + + + + + + + + + + A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and +the a supports either the existence of b, or the truth value of b. + + + is evidence for + + + + + + + + + + + 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' + x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. + + + + + composed primarily of + + + + + + + + + + + ABal nucleus child nucleus of ABa nucleus (in C elegans) + c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d + + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. + child nucleus of + + + + + + + + + A child nucleus relationship in which the cells are part of a hermaphroditic organism + + child nucleus of in hermaphrodite + + + + + + + + + A child nucleus relationship in which the cells are part of a male organism + + child nucleus of in male + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + + + has part that occurs in + + + + + + + + + true + + + + + + + + + + + + + + An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y + Axiomatization to GO to be added later + + ubiquitinates + + + + + + + + + + is kinase activity + + + + + + + + + + is ubiquitination + + + + + + + + + + See notes for inverse relation + + receives input from + + + + + + + + + This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. + + sends output to + + + + + + + + + + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. + relation between physical entity and a process or stage + + + + + + + + + + + + + + + + + + x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). + + existence starts during + + + + + + + + + x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). + + existence starts with + + + + + + + + + x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence overlaps + + + + + + + + + + x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + + exists during + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts and ends during + + + + + + + + + + + + + + + + + + x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during + + + + + + + + + x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends with + + + + + + + + + + x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships + + transformation of + + + + + + + + + + x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t + + + immediate transformation of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts during or after + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during or before + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + towards + + + + + + + + + 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate + p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c + + has intermediate product + + has intermediate + + + + + + + + + + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between entities + + + + + + + + + + + + + + A coral reef environment is determined by a particular coral reef + s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. + The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future + + + determined by (system to material entity) + + + + determined by + + + + + + + + + inverse of determined by + + determines (material entity to system) + + + determines + + + + + + + + + + + + + + + + s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. + + + determined by part of + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + + + + + + x is transcribed from y if and only if x is synthesized from template y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + transcribed from + + + + + + + + + inverse of transcribed from + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + transcribed to + + + + + + + + + + + + + + + + + + + + + + + + + + x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + ribosomal translation of + + + + + + + + + + + + + + + + + + + + + + + + + inverse of ribosomal translation of + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + ribosomally translates to + + + + + + + + + + A relation that holds between two entities that have the property of being sequences or having sequences. + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. + The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. + + sequentially related to + + + + + + + + + Every UTR is adjacent to a CDS of the same transcript + Two consecutive DNA residues are sequentially adjacent + Two exons on a processed transcript that were previously connected by an intron are adjacent + x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + sequentially adjacent to + + + + + + + + + + + Every CDS has as a start sequence the start codon for that transcript + x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence + + started by + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has start sequence + + + + + + + + + + inverse of has start sequence + + starts + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + + is start sequence of + + + + + + + + + + + Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) + x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence + + ended by + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has end sequence + + + + + + + + + + inverse of has end sequence + + ends + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + + is end sequence of + + + + + + + + + x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. + In the SO paper, this was defined as an instance-type relation + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + is consecutive sequence of + + + + + + + + + + Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. + x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering + + + is sequentially aligned with + + + + + + + + + + + The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) + x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + + + bounds sequence of + + + + + + + + + + inverse of bounds sequence of + + + + is bound by sequence of + + + + + + + + + + + + + x has subsequence y iff all of the sequence parts of y are sequence parts of x + + contains + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has subsequence + + + + + + + + + + + + inverse of has subsequence + + contained by + + + is subsequence of + + + + + + + + + + + + + + + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + + + overlaps sequence of + + + + + + + + + + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + + disconnected from + + does not overlap sequence of + + + + + + + + + + inverse of downstream of sequence of + + + is upstream of sequence of + + + + + + + + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + + + is downstream of sequence of + + + + + + + + + + A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript + x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y + + + + is immediately downstream of sequence of + + + + + + + + + + A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript + inverse of immediately downstream of + + + is immediately upstream of sequence of + + + + + + + + + + + + + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' + A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. + + has supporting framework + The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). + has skeleton + + + + + + This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. + + + + + + + + + + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. + + results in ending of + + + + + + + + + + + + + + x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y + Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism + + http://eol.org/schema/terms/hyperparasitoidOf + https://en.wikipedia.org/wiki/Hyperparasite + hyperparasitoid of + epiparasite of + + hyperparasite of + + + + + + + + + + + + + inverse of hyperparasite of + + has epiparasite + has hyperparasite + hyperparasitoidized by + + + hyperparasitized by + + + + + + + + + + http://en.wikipedia.org/wiki/Allelopathy + + allelopath of + http://eol.org/schema/terms/allelopathyYes + x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y + + + + + + + + + + + + pathogen of + + + + + + + + + + + has pathogen + + + + + + + + + inverse of is evidence for + + + + + x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. + has evidence + + + + + + + + + + + + causally influenced by (entity-centric) + causally influenced by + + + + + + + + + + interaction relation helper property + + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + + molecular interaction relation helper property + + + + + + + + + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c + + + + + + results in movement of + + + + + + + + + + + + + + + + + + + + + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). + + + + causally influences (entity-centric) + causally influences + + + + + + + + + + + A relation that holds between elements of a musculoskeletal system or its analogs. + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. + biomechanically related to + + + + + + + + + m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. + + Wikipedia:Antagonist_(muscle) + has muscle antagonist + + + + + + + + + + + inverse of branching part of + + + + has branching part + + + + + + + + + + + x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. + + UBERON:cjm + This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. + + conduit for + + + + + + + + + + x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. + + GOC:cjm + + lumen of + + + + + + + + + + s is luminal space of x iff s is lumen_of x and s is an immaterial entity + + + luminal space of + + + + + + + + + + A relation that holds between an attribute or a qualifier and another attribute. + + + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. + + has modifier + + + + + + + + + + + + + participates in a biotic-biotic interaction with + + + + + + + + + + + + inverse of has skeleton + + + skeleton of + + + + + + + + + + p directly regulates q iff p is immediately causally upstream of q and p regulates q. + + + directly regulates (processual) + + + + + directly regulates + + + + + + + + + holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y). + existence starts at end of + + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + + has part structure that is capable of + + + + + + + + + + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. + results in closure of + + + + + + + + + p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p + results in breakdown of + + + + + + + + + results in synthesis of + + + + + + + + + + + + + results in assembly of + + + + + + + + + p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. + results in catabolism of + + + + + + + + + + results in disassembly of + + + + + + + + + + results in remodeling of + + + + + + + + + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c + results in organization of + + + + + + + + + holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y). + existence ends at start of + + + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + + pazopanib -> pathological angiogenesis + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. + treats + + The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. + capable of inhibiting or preventing pathological process + + + + + treats + Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + + + + + + + + + benzene -> cancer [CHEBI] + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. + causes disease + + capable of upregulating or causing pathological process + + + + + + + + + c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. + treats + + is substance that treats + + + + + + + + + + c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. + May be ceded to OBI + is marker for + + + + + + + + + Inverse of 'causal agent in process' + + process has causal agent + + + + + + + + A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + obsolete related via dependence to + true + + + + + + + + A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Groups both positive and negative correlation + correlated with + + + + + + + + + An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. + A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. + In the Gene Ontology association model, this corresponds to the With/From field + is evidence with support from + + + + + + + + + Inverse of is-model-of + has model + + + + + + + + Do not use this relation directly. It is a grouping relation. + related via evidence or inference to + + + + + + + + + + visits + https://github.com/oborel/obo-relations/issues/74 + + + + + + + + + visited by + + + + + + + + + + visits flowers of + + + + + + + + + has flowers visited by + + + + + + + + + + + lays eggs in + + + + + + + + + + has eggs laid in by + + + + + + + + + + https://github.com/jhpoelen/eol-globi-data/issues/143 + kills + + + + + + + + + is killed by + + + + + + + + + + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. + + directly positively regulates (process to process) + + + + + directly positively regulates + + + + + + + + + + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. + + directly negatively regulates (process to process) + + + + + directly negatively regulates + + + + + + + + + + A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host + + ectoparasite of + + + + + + + + + inverse of ectoparasite of + + has ectoparasite + + + + + + + + + + + A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system + lives inside of + endoparasite of + + + + + + + + + has endoparasite + + + + + + + + + + A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite + mesoparasite of + + + + + + + + + inverse of mesoparasite of + + has mesoparasite + + + + + + + + + + A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. + + intercellular endoparasite of + + + + + + + + + inverse of intercellular endoparasite of + + has intercellular endoparasite + + + + + + + + + + A sub-relation of endoparasite-of in which the parasite inhabits host cells. + + intracellular endoparasite of + + + + + + + + + inverse of intracellular endoparasite of + + has intracellular endoparasite + + + + + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + + co-roosts with + + + + + + + + + + + + + + + + + + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + + + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + produces + + + + + + + + + + + a produced_by b iff some process that occurs_in b has_output a. + + + produced by + + + + + + + + + + + Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. + + represses expression of + + + + + + + + + + + Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. + + increases expression of + + + + + + + + + + A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + + is used to study + The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. + has role in modeling + + + + + + + + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + causes or contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. + causes condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. + contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. + contributes to expressivity of condition + contributes to severity of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. + contributes to penetrance of condition + contributes to frequency of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. + is preventative for condition + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + ameliorates condition + + + + + + + + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + + + + + + + + + A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. + exacerbates condition + + + + + + + + + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. + condition ameliorated by + + + + + + + + + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. + condition exacerbated by + + + + + + + + + + + + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a more specific relations + + 2017-11-05T02:38:20Z + condition has genetic basis in + + + + + + + + + + + 2017-11-05T02:45:20Z + has material basis in gain of function germline mutation in + + + + + + + + + + + + + 2017-11-05T02:45:37Z + has material basis in loss of function germline mutation in + + + + + + + + + + + 2017-11-05T02:45:54Z + has material basis in germline mutation in + + + + + + + + + + + + 2017-11-05T02:46:07Z + has material basis in somatic mutation in + + + + + + + + + + + + 2017-11-05T02:46:26Z + has major susceptibility factor + + + + + + + + + + + 2017-11-05T02:46:57Z + has partial material basis in germline mutation in + + + + + + + + + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. + + 2018-12-13T11:26:17Z + + has primary input or output + + + + + + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + + 2018-12-13T11:26:32Z + + has primary output + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + + 2018-12-13T11:26:56Z + + has primary input + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a more specific relations + + 2017-11-05T02:53:08Z + is genetic basis for condition + + + + + + + + + Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:55:51Z + is causal gain of function germline mutation of in + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:56:06Z + is causal loss of function germline mutation of in + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:56:40Z + is causal germline mutation in + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:57:07Z + is causal somatic mutation in + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. + + 2017-11-05T02:57:43Z + is causal susceptibility factor for + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. + + 2017-11-05T02:58:43Z + is causal germline mutation partially giving rise to + + + + + + + + + + + + 2017-11-05T03:20:01Z + realizable has basis in + + + + + + + + + + 2017-11-05T03:20:29Z + is basis for realizable + + + + + + + + + + + + 2017-11-05T03:26:47Z + disease has basis in + + + + + + + + + + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) + + 2017-11-05T03:29:32Z + disease has basis in dysfunction of + + + + + + + + + + A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) + + 2017-11-05T03:37:52Z + disease has basis in disruption of + + + + + + + + + + + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. + + 2017-11-05T03:46:07Z + disease has basis in feature + + + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. + + 2017-11-05T03:50:54Z + causal relationship with disease as subject + + + + + + + + + + + + + + + + + + + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) + + 2017-11-05T03:51:09Z + disease causes disruption of + + + + + + + + + + + + + + + disease causes dysfunction of (disease to anatomical entity) + + 2017-11-05T03:58:20Z + disease causes dysfunction of + + + + + + + + + + + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. + TODO: complete range axiom once more of CARO has been mireoted in to this ontology + This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. + + 2017-11-05T04:06:02Z + disease has location + + + + + + + + + + + + + + + + + + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity + + 2017-12-26T19:37:31Z + disease has inflammation site + + + + + + + + + + + + + + + A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. + + 2017-12-26T19:45:49Z + realized in response to stimulus + + + + + + + + + + + + + + + + + + A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. + + 2017-12-26T19:50:53Z + disease has feature + + + + + + + + + + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. + + 2017-12-26T19:58:44Z + disease arises from alteration in structure + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + + 2018-01-25T23:20:13Z + enables subfunction + + + + + + + + + + + + + + + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. + DEPRECATED inheres in + true + + + + + + + + DEPRECATED bearer of + true + + + + + + + + A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity. + + has driver + + + + + + + + + + A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes. + + has disease driver + + + + + + + + + + + An interaction relationship wherein a plant or algae is living on the outside surface of another plant. + https://en.wikipedia.org/wiki/Epiphyte + epiphyte of + + + + + + + + + inverse of epiphyte of + + has epiphyte + + + + + + + + + + A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material + https://en.wikipedia.org/wiki/Kleptoparasitism + kleptoparasite of + + + + + + + + + inverse of kleptoparasite of + + kleptoparasitized by + + + + + + + + + + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. + creates habitat for + + + + + + + + + + + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. + ecologically co-occurs with + + + + + + + + + + An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. + lays eggs on + + + + + + + + + inverse of lays eggs on + has eggs laid on by + + + + + + + + + + + muffin 'has substance added' some 'baking soda' + + "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. + The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. + + has substance added + + + + + + + + + + + 'egg white' 'has substance removed' some 'egg yolk' + + "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. + + has substance removed + + + + + + + + + + + sardines 'immersed in' some 'oil and mustard' + + "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + + immersed in + + + + + + + + + + sardine has consumer some homo sapiens + + 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. + + has consumer + + + + + + + + + + bread 'has primary substance added' some 'flour' + + 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. + + has primary substance added + + + + + + + + + + + + + + + A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. + An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) + Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. + r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. + + + + + triggered by process + realized in response to + https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit + + + + + triggered by process + RO:cjm + + + + + + + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + + regulates activity of + + + + + + + + + + + The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. + + regulates quantity of + + + + + + + + + + + The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. + + indirectly regulates activity of + + + + + + + + + + + The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. + +For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. + + decreases by repression quantity of + + + + + + + + + + + The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. + +For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. + + increases by expression quantity of + + + + + + + + + + + The entity A has an activity that directly positively regulates the quantity of B. + + directly positively regulates quantity of + + + + + + + + + + + The entity A has an activity that directly negatively regulates the quantity of B. + + directly negatively regulates quantity of + + + + + + + + + + + The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. + + indirectly activates + indirectly positively regulates activity of + + + + + + + + + + + AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) + An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. + + destabilizes quantity of + + + + + + + + + + + AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) + An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. + + stabilizes quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. + + indirectly inhibits + indirectly negatively regulates activity of + + + + + + + + + The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. + + directly regulates quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. + + indirectly regulates quantity of + + + + + + + + + The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. + + indirectly negatively regulates quantity of + + + + + + + + + The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. + + indirectly positively regulates quantity of + + + + + + + + + + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg + 2020-04-22T20:27:26Z + has small molecule regulator + + + + + + + + + + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg + 2020-04-22T20:28:37Z + has small molecule activator + + + + + + + + + + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg + 2020-04-22T20:28:54Z + has small molecule inhibitor + + + + + + + + + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg + 2020-06-08T17:21:33Z + + + + acts on population of + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg + 2020-06-24T13:15:17Z + is small molecule regulator of + + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg + 2020-06-24T13:15:26Z + is small molecule activator of + + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg + 2020-06-24T13:15:35Z + is small molecule inhibitor of + + + + + + + + + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg + 2020-08-27T08:13:59Z + results in adhesion of + + + + + + + + + pg + 2021-02-26T07:28:29Z + + + + results in fusion of + + + + + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + + + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + + + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. + + 2020-07-17T09:26:52Z + has synaptic input or output in + has synaptic IO in region + + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. + + 2020-07-17T09:42:23Z + receives synaptic input in region + + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. + + 2020-07-17T09:45:06Z + sends synaptic output to region + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:52:19Z + has synaptic IO throughout + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:55:36Z + receives synaptic input throughout + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:57:27Z + sends synaptic output throughout + + + + + + + + + + + + + + Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. + + 2020-07-20T12:10:09Z + has sensory dendrite location + has sensory terminal in + has sensory terminal location + has sensory dendrite in + + + + + + + + + + A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. + + 2021-05-26T08:40:18Z + receives synaptic input from neuron + + + + + + + + + A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. + + 2021-05-26T08:41:07Z + Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. + sends synaptic output to cell + + + + + + + + + A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. + + disease has infectious agent + + + + + + + + + + + + + + transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) + A relation between a material entity and some data in which the data is taken as exemplifying the material entity. + C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. + + This relation is not meant to capture the relation between occurrents and data. + has exemplar data + + + + + + + + + + exemplar data of + + + + + + + + + + A relation between a group and another group it is part of but does not fully constitute. + X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. + + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. + subcluster of + + + + + + + + + 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1'). + transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3. + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + + + + + + + q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + different in magnitude relative to + + + + + q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + + + q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + increased in magnitude relative to + + + + + q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + + + q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + decreased in magnitude relative to + + + + + q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + similar in magnitude relative to + + + + + q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + has relative magnitude + + + + + + + + s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. + Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. + has cross section + + + + + s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + reciprocal of + + + + + q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + + 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') + A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. + + + has high plasma membrane amount + + + + + A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. + PMID:19243617 + + + + + + + + + + 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') + A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. + + + has low plasma membrane amount + + + + + A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. + PMID:19243617 + + + + + + + + Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. + + 2021-11-05T17:30:14Z + has phenotype or disease + https://github.com/oborel/obo-relations/issues/478 + + + + + + + + + A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. + + 2021-11-05T17:30:44Z + has disease + https://github.com/oborel/obo-relations/issues/478 + + + + + + + + + X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. + ExO:0000083 + 2021-12-14T20:41:45Z + + has exposure medium + + + + + + + + + + + + A diagnostic testing device utilizes a specimen. + X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. + + + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08T12:00:00Z + utilizes + device utilizes material + + + + + + + + + Helper relation for OWL definition of RO:0018002 myristoylates + + is myristoyltransferase activity + + + + + + + + + + + + + + + A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input + + + myristoylates + + + + + + + + inverse of myristoylates + + myristoylated by + + + + + + + + + mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor + + is agonist of + + + + + + + + + + pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level + + is inverse agonist of + + + + + + + + + + tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level + + is antagonist of + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + negatively regulates characteristic + + + + + + + + + Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. + + confers susceptibility to condition + + + + + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + + 2018-09-26T00:00:32Z + disease relationship + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + + 2018-09-26T01:08:58Z + results in changes to anatomical or cellular structure + + + + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + TODO: Add homeomorphy axiom + + + + + ECO:0000041 + SO:similar_to + sameness + similar to + correspondence + resemblance + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + + + + + + + + + + + + Similarity that results from common evolutionary origin. + + + homologous to + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + + + + + + + + + + + + + Similarity that results from independent evolution. + + + homoplasous to + analogy + in homoplasy relationship with + + + + + + Similarity that results from independent evolution. + + + + + + + + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + ECO:0000075 + homocracous to + Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + in homocracy relationship with + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + + + + + + + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + analogy + Convergence usually implies a notion of adaptation. + in convergence relationship with + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + + + + + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + parallel evolution + Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + in parallelism relationship with + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + + + + + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + ECO:0000071 + MI:2163 + structural homologous to + idealistic homology + in structural homology relationship with + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by common descent. + + + homology + ECO:0000080 + RO_proposed_relation:homologous_to + SO:0000330 + SO:0000853 + SO:0000857 + SO:homologous_to + TAO:homologous_to + cladistic homology + historical homologous to + phylogenetic homology + taxic homology + true homology + in historical homology relationship with + + + + + + Homology that is defined by common descent. + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + ECO:0000067 + biological homologous to + transformational homology + Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + in biological homology relationship with + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + + + + + + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + atavism + rudiment + reversion + in reversal relationship with + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + + + + + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + + MeSH:Synteny + SO:0000860 + SO:0005858 + syntenic homologous to + synteny + in syntenic homology relationship with + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + MeSH:Synteny + + + + + + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + SO:0000854 + SO:0000859 + SO:paralogous_to + paralogous to + in paralogy relationship with + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + + + + + + + + + + + + + Paralogy that involves sets of syntenic blocks. + + + syntenic paralogous to + duplicon + paralogon + in syntenic paralogy relationship with + + + + + + Paralogy that involves sets of syntenic blocks. + + + DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y + + + + + + + + + + Syntenic homology that involves chromosomes of different species. + + + syntenic orthologous to + in syntenic orthology relationship with + + + + + + Syntenic homology that involves chromosomes of different species. + + + + + + + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + + fractional homology + partial homologous to + segmental homology + mixed homology + modular homology + partial correspondence + percent homology + in partial homology relationship with + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + ISBN:0123195837 + ISBN:978-0471984931 + + + + + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + MeSH:Structural_Homology,_Protein + protein structural homologous to + in protein structural homology relationship with + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + + + + + + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + + pseudogene + SO:non_functional_homolog_of + non functional homologous to + in non functional homology relationship with + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + SO:non_functional_homolog_of + + + + + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + ECO:00000060 + SO:0000855 + SO:0000858 + SO:orthologous_to + orthologous to + The term is sometimes also used for anatomical structures. + in orthology relationship with + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + + + + + + + + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + xenologous to + The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + in xenology relationship with + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + + + + + + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + + 1 to 1 homologous to + 1:1 homology + one-to-one homology + in 1 to 1 homology relationship with + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + BGEE:curator + + + + + + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + 1 to 1 orthologous to + 1:1 orthology + one-to-one orthology + in 1 to 1 orthology relationship with + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + + + + + + + + + + + Paralogy that results from a whole genome duplication event. + + + ohnologous to + homoeology + in ohnology relationship with + + + + + + Paralogy that results from a whole genome duplication event. + + + + + + + + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + in-paralogous to + inparalogy + symparalogy + in in-paralogy relationship with + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + + + + + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + alloparalogy + out-paralogous to + outparalogy + in out-paralogy relationship with + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + + + + + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + pro-orthologous to + in pro-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + + + + + + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + semi-orthologous to + The converse of pro-orthologous. + in semi-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + + + + + + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + serial homologous to + homonomy + in serial homology relationship with + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + + + + + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + + heterochronous homologous to + heterochrony + in heterochronous homology relationship with + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + ISBN:978-0674639416 + + + + + + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + juvenification + pedomorphosis + in paedomorphorsis relationship with + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + ISBN:978-0674639416 + + + + + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + in peramorphosis relationship with + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + + + + + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + in progenesis relationship with + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + ISBN:978-0674639416 + + + + + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + juvenilization + neotenous to + in neoteny relationship with + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + ISBN:978-0674639416 + + + + + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + mimicrous to + in mimicry relationship with + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + + + + + + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + 1 to many orthologous to + 1:many orthology + one-to-many orthology + co-orthology + many to 1 orthology + in 1 to many orthology relationship with + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + + + + + + + + + + + Historical homology that involves two members of a larger set of homologs. + + + many to many homologous to + many-to-many homology + many:many homology + in many to many homology relationship with + + + + + + Historical homology that involves two members of a larger set of homologs. + + + + + + + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + + 1 to many homologous to + one-to-many homology + 1:many homology + in 1 to many homology relationship with + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + BGEE:curator + + + + + + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + + apomorphous to + synapomorphy + in apomorphy relationship with + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + ISBN:978-0252068140 + + + + + + + + + + Historical homology that is based on distant shared ancestry. + + + plesiomorphous to + symplesiomorphy + This term is usually contrasted to apomorphy. + in plesiomorphy relationship with + + + + + + Historical homology that is based on distant shared ancestry. + + ISBN:978-0252068140 + + + + + + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + deep genetic homology + deep homologous to + generative homology + homoiology + Used for structures in distantly related taxa. + in deep homology relationship with + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + + + + + + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + hemiplasous to + in hemiplasy relationship with + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + + + + + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + gametologous to + in gametology relationship with + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + + + + + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + + MeSH:Chromosome_Pairing + chromosomal homologous to + in chromosomal homology relationship with + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + ISBN:0195307615 + + + + + + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + many to many orthologous to + many-to-many orthology + many:many orthology + trans-orthology + co-orthology + trans-homology + in many to many orthology relationship with + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + + + + + + + + + + + + Paralogy that involves genes from the same species. + + + within-species paralogous to + in within-species paralogy relationship with + + + + + + Paralogy that involves genes from the same species. + + + + + + + + + + + + Paralogy that involves genes from different species. + + + between-species paralogous to + The genes have diverged before a speciation event. + in between-species paralogy relationship with + + + + + + Paralogy that involves genes from different species. + + + + + + + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + post-displacement + in postdisplacement relationship with + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + + + + + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + in hypermorphosis relationship with + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + ISBN:978-0674639416 + + + + + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + synologous to + in synology relationship with + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + + + + + + + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + ECO:0000080 + isoorthologous to + in isoorthology relationship with + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + tandem paralogous to + iterative paralogy + serial paralogy + in tandem paralogy relationship with + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + ISBN:978-0878932665 + + + + + + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + apomorphic tendency + cryptic homology + latent homologous to + underlying synapomorphy + homoiology + homoplastic tendency + re-awakening + Used for structures in closely related taxa. + in latent homology relationship with + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + + + ISBN:0199141118 + + + + + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + generative homology + syngenous to + Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + in syngeny relationship with + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R + + + + + + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + 1:1 paralogy + apparent 1:1 orthology + apparent orthologous to + pseudoorthology + The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + in apparent orthology relationship with + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + + + + + + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + pseudoparalogous to + These genes may come out as paralogs in a single-genome analysis. + in pseudoparalogy relationship with + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + + + + + + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + equivalogous to + This may include examples of orthology, paralogy and xenology. + in equivalogy relationship with + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + interologous to + in interology relationship with + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + + + + + + + + + + + Similarity that is characterized by interchangeability in function. + + + functional similarity + in functional equivalence relationship with + + + + + + Similarity that is characterized by interchangeability in function. + + + + + + + + + + + + + Biological homology that involves parts of the same organism. + + + iterative homologous to + in iterative homology relationship with + + + + + + Biological homology that involves parts of the same organism. + + + + + + + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + duplicate xenology + multiple xenology + paraxenologous to + in paraxenology relationship with + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + + + + + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + plerologous to + This phenomenon is usually due to gene conversion process. + in plerology relationship with + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + + + + + + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + homotopous to + Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + in homotopy relationship with + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + + ISBN:0123195837 + + + + + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + heterotopy + in homeosis relationship with + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + + + + + + + + + + + + Synology that results from allopolyploidy. + + + homoeologous to + On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + in homoeology relationship with + + + + + + Synology that results from allopolyploidy. + + + + + + + + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + axis paramorphism + in paramorphism relationship with + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + + + + + + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + regulogous to + in regulogy relationship with + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + + + 100 + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + dos + 2018-05-22T16:43:28Z + This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. + has increased age-specific mortality rate + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + PMID:24138933 + Wikipedia:Infant_mortality + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + spatial region + + + + + + + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + + disposition + + + + + + + + + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + + + + + + + + + + + + + + + quality + + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + + + + + + + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + generically dependent continuant + + + + + + + + + function + + + + + + + + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + + + + + + + immaterial entity + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + CARO:0000000 + Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. + anatomical entity + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + CAROC:Brownsville2014 + + + + + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. + connected anatomical structure + + + + + + + + + + + + + + + + An anatomical entity that has mass. + CARO:0000006 + material anatomical entity + + + + + + + + + + + + + + + + Anatomical entity that has no mass. + CARO:0000007 + immaterial anatomical entity + + + + + + + + + A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. + CARO:0001001 + neuron projection bundle + + + + + + + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + Melissa Haendel + organism or virus or viroid + + + + + + + + + An anatomical structure that has more than one cell as a part. + djs93 + CARO:0010000 + multicellular anatomical structure + + + + + + + + + + + + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CALOHA:TS-2035 + FBbt:00007002 + FMA:68646 + GO:0005623 + KUPO:0000002 + MESH:D002477 + VHOG:0001533 + WBbt:0004017 + XAO:0003012 + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + cell + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CARO:mah + + + + + + + + + Any neuron having a sensory function; an afferent neuron conveying sensory impulses. + BTO:0001037 + FBbt:00005124 + FMA:84649 + MESH:D011984 + WBbt:0005759 + sensory neuron + + + + + Any neuron having a sensory function; an afferent neuron conveying sensory impulses. + ISBN:0721662544 + + + + + + + + + + The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. + + BTO:0000938 + CALOHA:TS-0683 + FBbt:00005106 + FMA:54527 + VHOG:0001483 + WBbt:0003679 + nerve cell + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. + neuron + + + + + The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. + MESH:D009474 + http://en.wikipedia.org/wiki/Neuron + + + + + + + + + A system which has the disposition to environ one or more material entities. + 2013-09-23T16:04:08Z + EcoLexicon:environment + environment + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + + A system which has the disposition to environ one or more material entities. + DOI:10.1186/2041-1480-4-43 + + + + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + molecular function + GO:0003674 + Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + molecular_function + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + GOC:pdt + + + + + + + + + + + + true + + + Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. + KEGG_REACTION:R03876 + Reactome:R-HSA-1169394 + Reactome:R-HSA-1169395 + Reactome:R-HSA-1169397 + Reactome:R-HSA-1169398 + Reactome:R-HSA-1169402 + Reactome:R-HSA-1169405 + Reactome:R-HSA-1169406 + Reactome:R-HSA-1234163 + Reactome:R-HSA-1234172 + Reactome:R-HSA-1253282 + Reactome:R-HSA-1358789 + Reactome:R-HSA-1358790 + Reactome:R-HSA-1358792 + Reactome:R-HSA-1363331 + Reactome:R-HSA-168915 + Reactome:R-HSA-173542 + Reactome:R-HSA-173545 + Reactome:R-HSA-174057 + Reactome:R-HSA-174104 + Reactome:R-HSA-174144 + Reactome:R-HSA-174159 + Reactome:R-HSA-174195 + Reactome:R-HSA-174227 + Reactome:R-HSA-179417 + Reactome:R-HSA-180540 + Reactome:R-HSA-180597 + Reactome:R-HSA-182986 + Reactome:R-HSA-182993 + Reactome:R-HSA-183036 + Reactome:R-HSA-183051 + Reactome:R-HSA-183084 + Reactome:R-HSA-183089 + Reactome:R-HSA-1852623 + Reactome:R-HSA-187575 + Reactome:R-HSA-1912357 + Reactome:R-HSA-1912386 + Reactome:R-HSA-1918092 + Reactome:R-HSA-1918095 + Reactome:R-HSA-1977296 + Reactome:R-HSA-1980074 + Reactome:R-HSA-1980118 + Reactome:R-HSA-201425 + Reactome:R-HSA-202453 + Reactome:R-HSA-202534 + Reactome:R-HSA-205118 + Reactome:R-HSA-209063 + Reactome:R-HSA-211734 + Reactome:R-HSA-2169050 + Reactome:R-HSA-2172172 + Reactome:R-HSA-2179276 + Reactome:R-HSA-2186747 + Reactome:R-HSA-2186785 + Reactome:R-HSA-2187368 + Reactome:R-HSA-2213017 + Reactome:R-HSA-264444 + Reactome:R-HSA-2682349 + Reactome:R-HSA-2730904 + Reactome:R-HSA-2737728 + Reactome:R-HSA-2769007 + Reactome:R-HSA-2900765 + Reactome:R-HSA-3000335 + Reactome:R-HSA-3134804 + Reactome:R-HSA-3134946 + Reactome:R-HSA-3249386 + Reactome:R-HSA-3780995 + Reactome:R-HSA-3781009 + Reactome:R-HSA-3788724 + Reactome:R-HSA-3797226 + Reactome:R-HSA-400267 + Reactome:R-HSA-4332236 + Reactome:R-HSA-446877 + Reactome:R-HSA-450358 + Reactome:R-HSA-451418 + Reactome:R-HSA-5205682 + Reactome:R-HSA-5357757 + Reactome:R-HSA-5362412 + Reactome:R-HSA-5483238 + Reactome:R-HSA-5607725 + Reactome:R-HSA-5607728 + Reactome:R-HSA-5607756 + Reactome:R-HSA-5607757 + Reactome:R-HSA-5610742 + Reactome:R-HSA-5610745 + Reactome:R-HSA-5610746 + Reactome:R-HSA-5652009 + Reactome:R-HSA-5655170 + Reactome:R-HSA-5660753 + Reactome:R-HSA-5667107 + Reactome:R-HSA-5667111 + Reactome:R-HSA-5668454 + Reactome:R-HSA-5668534 + Reactome:R-HSA-5675470 + Reactome:R-HSA-5684250 + Reactome:R-HSA-5691108 + Reactome:R-HSA-5693108 + Reactome:R-HSA-69598 + Reactome:R-HSA-741386 + Reactome:R-HSA-75824 + Reactome:R-HSA-870449 + Reactome:R-HSA-8948709 + Reactome:R-HSA-8956106 + Reactome:R-HSA-9013069 + Reactome:R-HSA-9013974 + Reactome:R-HSA-9014342 + Reactome:R-HSA-918224 + Reactome:R-HSA-936412 + Reactome:R-HSA-936942 + Reactome:R-HSA-936986 + Reactome:R-HSA-9628444 + Reactome:R-HSA-9645394 + Reactome:R-HSA-9645414 + Reactome:R-HSA-9688831 + Reactome:R-HSA-9701000 + Reactome:R-HSA-975118 + Reactome:R-HSA-975147 + Reactome:R-HSA-983140 + Reactome:R-HSA-983153 + Reactome:R-HSA-983156 + anaphase-promoting complex activity + ubiquitin conjugating enzyme activity + ubiquitin ligase activity + ubiquitin protein ligase activity + ubiquitin protein-ligase activity + ubiquitin-conjugating enzyme activity + E2 + E3 + GO:0004842 + ubiquitin-protein transferase activity + + + + + Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. + GOC:BioGRID + GOC:jh2 + PMID:9635407 + + + + + Reactome:R-HSA-1169394 + ISGylation of IRF3 + + + + + Reactome:R-HSA-1169395 + ISGylation of viral protein NS1 + + + + + Reactome:R-HSA-1169397 + Activation of ISG15 by UBA7 E1 ligase + + + + + Reactome:R-HSA-1169398 + ISGylation of host protein filamin B + + + + + Reactome:R-HSA-1169402 + ISGylation of E2 conjugating enzymes + + + + + Reactome:R-HSA-1169405 + ISGylation of protein phosphatase 1 beta (PP2CB) + + + + + Reactome:R-HSA-1169406 + ISGylation of host proteins + + + + + Reactome:R-HSA-1234163 + Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha + + + + + Reactome:R-HSA-1234172 + Nuclear VBC complex ubiquitinylates HIF-alpha + + + + + Reactome:R-HSA-1253282 + ERBB4 ubiquitination by WWP1/ITCH + + + + + Reactome:R-HSA-1358789 + Self-ubiquitination of RNF41 + + + + + Reactome:R-HSA-1358790 + RNF41 ubiquitinates ERBB3 + + + + + Reactome:R-HSA-1358792 + RNF41 ubiquitinates activated ERBB3 + + + + + Reactome:R-HSA-1363331 + Ubiquitination of p130 (RBL2) by SCF (Skp2) + + + + + Reactome:R-HSA-168915 + K63-linked ubiquitination of RIP1 bound to the activated TLR complex + + + + + Reactome:R-HSA-173542 + SMURF2 ubiquitinates SMAD2 + + + + + Reactome:R-HSA-173545 + Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling + + + + + Reactome:R-HSA-174057 + Multiubiquitination of APC/C-associated Cdh1 + + + + + Reactome:R-HSA-174104 + Ubiquitination of Cyclin A by APC/C:Cdc20 complex + + + + + Reactome:R-HSA-174144 + Ubiquitination of Securin by phospho-APC/C:Cdc20 complex + + + + + Reactome:R-HSA-174159 + Ubiquitination of Emi1 by SCF-beta-TrCP + + + + + Reactome:R-HSA-174195 + Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex + + + + + Reactome:R-HSA-174227 + Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex + + + + + Reactome:R-HSA-179417 + Multiubiquitination of Nek2A + + + + + Reactome:R-HSA-180540 + Multi-ubiquitination of APOBEC3G + + + + + Reactome:R-HSA-180597 + Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex + + + + + Reactome:R-HSA-182986 + CBL-mediated ubiquitination of CIN85 + + + + + Reactome:R-HSA-182993 + Ubiquitination of stimulated EGFR (CBL) + + + + + Reactome:R-HSA-183036 + Ubiquitination of stimulated EGFR (CBL:GRB2) + + + + + Reactome:R-HSA-183051 + CBL ubiquitinates Sprouty + + + + + Reactome:R-HSA-183084 + CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix + + + + + Reactome:R-HSA-183089 + CBL binds and ubiquitinates phosphorylated Sprouty + + + + + Reactome:R-HSA-1852623 + Ubiquitination of NICD1 by FBWX7 + + + + + Reactome:R-HSA-187575 + Ubiquitination of phospho-p27/p21 + + + + + Reactome:R-HSA-1912357 + ITCH ubiquitinates DTX + + + + + Reactome:R-HSA-1912386 + Ubiquitination of NOTCH1 by ITCH in the absence of ligand + + + + + Reactome:R-HSA-1918092 + CHIP (STUB1) mediates ubiquitination of ERBB2 + + + + + Reactome:R-HSA-1918095 + CUL5 mediates ubiquitination of ERBB2 + + + + + Reactome:R-HSA-1977296 + NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer + + + + + Reactome:R-HSA-1980074 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 + + + + + Reactome:R-HSA-1980118 + ARRB mediates NOTCH1 ubiquitination + + + + + Reactome:R-HSA-201425 + Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling + + + + + Reactome:R-HSA-202453 + Auto-ubiquitination of TRAF6 + + + + + Reactome:R-HSA-202534 + Ubiquitination of NEMO by TRAF6 + + + + + Reactome:R-HSA-205118 + TRAF6 polyubiquitinates NRIF + + + + + Reactome:R-HSA-209063 + Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex + + + + + Reactome:R-HSA-211734 + Ubiquitination of PAK-2p34 + + + + + Reactome:R-HSA-2169050 + SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7 + + + + + Reactome:R-HSA-2172172 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH2 + + + + + Reactome:R-HSA-2179276 + SMURF2 monoubiquitinates SMAD3 + + + + + Reactome:R-HSA-2186747 + Ubiquitination of SKI/SKIL by RNF111/SMURF2 + + + + + Reactome:R-HSA-2186785 + RNF111 ubiquitinates SMAD7 + + + + + Reactome:R-HSA-2187368 + STUB1 (CHIP) ubiquitinates SMAD3 + + + + + Reactome:R-HSA-2213017 + Auto-ubiquitination of TRAF3 + + + + + Reactome:R-HSA-264444 + Autoubiquitination of phospho-COP1(Ser-387 ) + + + + + Reactome:R-HSA-2682349 + RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels + + + + + Reactome:R-HSA-2730904 + Auto-ubiquitination of TRAF6 + + + + + Reactome:R-HSA-2737728 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants + + + + + Reactome:R-HSA-2769007 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants + + + + + Reactome:R-HSA-2900765 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants + + + + + Reactome:R-HSA-3000335 + SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA + + + + + Reactome:R-HSA-3134804 + STING ubiquitination by TRIM32 or TRIM56 + + + + + Reactome:R-HSA-3134946 + DDX41 ubiquitination by TRIM21 + + + + + Reactome:R-HSA-3249386 + DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1 + + + + + Reactome:R-HSA-3780995 + NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2 + + + + + Reactome:R-HSA-3781009 + NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1 + + + + + Reactome:R-HSA-3788724 + Cdh1:APC/C ubiquitinates EHMT1 and EHMT2 + + + + + Reactome:R-HSA-3797226 + Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease) + + + + + Reactome:R-HSA-400267 + BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins + + + + + Reactome:R-HSA-4332236 + CBL neddylates TGFBR2 + + + + + Reactome:R-HSA-446877 + TRAF6 is K63 poly-ubiquitinated + + + + + Reactome:R-HSA-450358 + Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation + + + + + Reactome:R-HSA-451418 + Pellino ubiquitinates IRAK1 + + + + + Reactome:R-HSA-5205682 + Parkin promotes the ubiquitination of mitochondrial substrates + + + + + Reactome:R-HSA-5357757 + BIRC(cIAP1/2) ubiquitinates RIPK1 + + + + + Reactome:R-HSA-5362412 + SYVN1 ubiquitinates Hh C-terminal fragments + + + + + Reactome:R-HSA-5483238 + Hh processing variants are ubiquitinated + + + + + Reactome:R-HSA-5607725 + SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP + + + + + Reactome:R-HSA-5607728 + beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex + + + + + Reactome:R-HSA-5607756 + TRAF6 oligomer autoubiquitinates + + + + + Reactome:R-HSA-5607757 + K63polyUb-TRAF6 ubiquitinates TAK1 + + + + + Reactome:R-HSA-5610742 + SCF(beta-TrCP) ubiquitinates p-GLI1 + + + + + Reactome:R-HSA-5610745 + SCF(beta-TrCP) ubiquitinates p-GLI2 + + + + + Reactome:R-HSA-5610746 + SCF(beta-TrCP) ubiquitinates p-GLI3 + + + + + Reactome:R-HSA-5652009 + RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA + + + + + Reactome:R-HSA-5655170 + RCHY1 monoubiquitinates POLH + + + + + Reactome:R-HSA-5660753 + SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA + + + + + Reactome:R-HSA-5667107 + SIAH1, SIAH2 ubiquitinate SNCAIP + + + + + Reactome:R-HSA-5667111 + PARK2 K63-Ubiquitinates SNCAIP + + + + + Reactome:R-HSA-5668454 + K63polyUb-cIAP1,2 ubiquitinates TRAF3 + + + + + Reactome:R-HSA-5668534 + cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK + + + + + Reactome:R-HSA-5675470 + BIRC2/3 (cIAP1/2) is autoubiquitinated + + + + + Reactome:R-HSA-5684250 + SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2 + + + + + Reactome:R-HSA-5691108 + SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2 + + + + + Reactome:R-HSA-5693108 + TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains + + + + + Reactome:R-HSA-69598 + Ubiquitination of phosphorylated Cdc25A + + + + + Reactome:R-HSA-741386 + RIP2 induces K63-linked ubiquitination of NEMO + + + + + Reactome:R-HSA-75824 + Ubiquitination of Cyclin D1 + + + + + Reactome:R-HSA-870449 + TRIM33 monoubiquitinates SMAD4 + + + + + Reactome:R-HSA-8948709 + DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3 + + + + + Reactome:R-HSA-8956106 + VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha + + + + + Reactome:R-HSA-9013069 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH3 + + + + + Reactome:R-HSA-9013974 + Auto-ubiquitination of TRAF3 within activated TLR3 complex + + + + + Reactome:R-HSA-9014342 + K63-linked ubiquitination of RIP1 bound to the activated TLR complex + + + + + Reactome:R-HSA-918224 + DDX58 is K63 polyubiquitinated + + + + + Reactome:R-HSA-936412 + RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS + + + + + Reactome:R-HSA-936942 + Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 + + + + + Reactome:R-HSA-936986 + Activated TRAF6 synthesizes unanchored polyubiquitin chains + + + + + Reactome:R-HSA-9628444 + Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation + + + + + Reactome:R-HSA-9645394 + Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation + + + + + Reactome:R-HSA-9645414 + Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer + + + + + Reactome:R-HSA-9688831 + STUB1 ubiquitinates RIPK3 at K55, K363 + + + + + Reactome:R-HSA-9701000 + BRCA1:BARD1 heterodimer autoubiquitinates + + + + + Reactome:R-HSA-975118 + TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex + + + + + Reactome:R-HSA-975147 + Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane + + + + + Reactome:R-HSA-983140 + Transfer of Ub from E2 to substrate and release of E2 + + + + + Reactome:R-HSA-983153 + E1 mediated ubiquitin activation + + + + + Reactome:R-HSA-983156 + Polyubiquitination of substrate + + + + + anaphase-promoting complex activity + GOC:dph + GOC:tb + + + + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + NIF_Subcellular:sao1702920020 + Wikipedia:Cell_nucleus + cell nucleus + horsetail nucleus + GO:0005634 + nucleus + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + GOC:go_curators + + + + + horsetail nucleus + GOC:al + GOC:mah + GOC:vw + PMID:15030757 + + + + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + jl + 2012-09-19T15:05:24Z + Wikipedia:Biological_process + biological process + physiological process + single organism process + single-organism process + GO:0008150 + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + biological_process + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + + + + + + true + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + Reactome:R-HSA-6788855 + Reactome:R-HSA-6788867 + phosphokinase activity + GO:0016301 + Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. + kinase activity + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + ISBN:0198506732 + + + + + Reactome:R-HSA-6788855 + FN3KRP phosphorylates PsiAm, RibAm + + + + + Reactome:R-HSA-6788867 + FN3K phosphorylates ketosamines + + + + + + + + + + + + true + + + Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. + Reactome:R-HSA-141367 + Reactome:R-HSA-162914 + GO:0019107 + myristoyltransferase activity + + + + + Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. + GOC:ai + + + + + Reactome:R-HSA-141367 + Myristoylation of tBID by NMT1 + + + + + Reactome:R-HSA-162914 + Myristoylation of Nef + + + + + + + + + A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. + disease + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATO:0000001 + quality + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + + A branchiness quality inhering in a bearer by virtue of the bearer's having branches. + + ramified + ramiform + PATO:0000402 + branched + + + + + A branchiness quality inhering in a bearer by virtue of the bearer's having branches. + WordNet:WordNet + + + + + + + + + A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. + PATO:0001199 + linear + + + + + A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. + ISBN:0881923214 + + + + + + + + + A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. + + 2009-10-06T04:37:14Z + PATO:0002124 + laminar + + + + + A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. + PATOC:GVG + + + + + + + + + An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, + An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. + A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. + This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. + + + 2017-06-05T17:55:39Z + exposure event or process + https://github.com/oborel/obo-relations/pull/173 + + + + + + + + + + + + + + Any entity that is ordered in discrete units along a linear axis. + + sequentially ordered entity + + + + + + + + + Any individual unit of a collection of like units arranged in a linear order + + An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. + sequence atomic unit + + + + + + + + + Any entity that can be divided into parts such that each part is an atomical unit of a sequence + + Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. + sequence bearer + + + + + + + + + A material entity consisting of multiple components that are causally integrated. + May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 + + http://www.jbiomedsem.com/content/4/1/43 + system + + + + + + + + + phenotype + + + + + + + + + + + + + + + + + + + ## Elucidation + +This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + +## How to interpret (informal) + +First the &quot;atemporal&quot; FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + axiom holds for all times + + + + + + + + ## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y) + relation has no temporal argument + + + + + + + + + curation status specification + + + + ready for release + + + + pending final vetting + + + + obsolescence reason specification + + + + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/ro.json b/ro.json index eec07263..ff13acf5 100644 --- a/ro.json +++ b/ro.json @@ -1,1288 +1,1860 @@ { "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro.json", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/description", + "val" : "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." + }, { + "pred" : "http://purl.org/dc/elements/1.1/title", + "val" : "OBO Relations Ontology" + }, { + "pred" : "http://purl.org/dc/terms/license", + "val" : "https://creativecommons.org/publicdomain/zero/1.0/" + }, { + "pred" : "http://www.w3.org/2002/07/owl#versionInfo", + "val" : "2023-02-19" + }, { + "pred" : "http://xmlns.com/foaf/0.1/homepage", + "val" : " https://github.com/oborel/obo-relations/" + } ], + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-19/ro.json" + }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/RO_0002291", + "id" : "http://purl.obolibrary.org/obo/BFO_0000002", + "lbl" : "continuant", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." - } ] - }, - "type" : "PROPERTY", - "lbl" : "ubiquitously expressed in" + "val" : "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "id" : "http://purl.obolibrary.org/obo/BFO_0000003", + "lbl" : "occurrent", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Inverse of 'expressed in'", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "PROPERTY", - "lbl" : "expresses" + "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "id" : "http://purl.obolibrary.org/obo/BFO_0000004", + "lbl" : "independent continuant", + "type" : "CLASS", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in formation of" + "definition" : { + "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "id" : "http://purl.obolibrary.org/obo/BFO_0000006", + "lbl" : "spatial region", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "lbl" : "process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000016", + "lbl" : "disposition", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "lbl" : "realizable entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000019", + "lbl" : "quality", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000020", + "lbl" : "specifically dependent continuant", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.", - "xrefs" : [ ] + "val" : "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000023", + "lbl" : "role", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000031", + "lbl" : "generically dependent continuant", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000034", + "lbl" : "function", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000040", + "lbl" : "material entity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + "val" : "my brain is part of my body (continuant parthood, two material entities)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in morphogenesis of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.", - "xrefs" : [ ] + "val" : "a core relation that holds between a whole and its part" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + "val" : "my body has part my brain (continuant parthood, two material entities)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in maturation of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002293", - "meta" : { - "definition" : { - "val" : "inverse of ubiquiotously expressed in", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "this year has part this day (occurrent parthood)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, - "type" : "PROPERTY", - "lbl" : "ubiquitously expresses" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002295", - "meta" : { - "definition" : { - "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in developmental progression of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realized in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + "val" : "this disease is realized in this disease course" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is realized in this shattering" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in development of" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000001", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "quality (PATO)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is realized in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is realized by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "realized_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] - }, - "type" : "CLASS", - "lbl" : "quality" + } }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", + "type" : "PROPERTY", "meta" : { + "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realizes" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease course realizes this disease" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:05:45Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation realizes this investigator role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this shattering realizes this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000060", + "lbl" : "obsolete preceded by", "type" : "PROPERTY", - "lbl" : "valid_for_gocam" + "meta" : { + "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Inverse of developmentally preceded by", - "xrefs" : [ ] + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] - }, - "type" : "PROPERTY", - "lbl" : "developmentally succeeded by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" } ] - }, - "type" : "PROPERTY", - "lbl" : "part of developmental precursor of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else", - "xrefs" : [ ] + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "occurs in" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "replaces" + "val" : "occurs_in" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds in" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds_in" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] - }, - "type" : "PROPERTY", - "lbl" : "developmentally replaces" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0019501", + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition.", - "xrefs" : [ ] + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-4142-7153" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "site of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] - }, - "type" : "PROPERTY", - "lbl" : "confers susceptibility to condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "id" : "http://purl.obolibrary.org/obo/BFO_0000141", + "lbl" : "immaterial entity", + "type" : "CLASS" + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000000", + "lbl" : "anatomical entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of has disposition", - "xrefs" : [ ] + "val" : "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.", + "xrefs" : [ "CAROC:Brownsville2014" ] }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "disposition of" + "comments" : [ "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure." ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "id" : "http://purl.obolibrary.org/obo/CARO_0000003", + "lbl" : "connected anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." + }, + "comments" : [ "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0000006", + "lbl" : "material anatomical entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence", - "xrefs" : [ ] + "val" : "An anatomical entity that has mass." } - }, - "type" : "PROPERTY", - "lbl" : "has disposition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "id" : "http://purl.obolibrary.org/obo/CARO_0000007", + "lbl" : "immaterial anatomical entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", - "xrefs" : [ "GOC:dos" ] + "val" : "Anatomical entity that has no mass." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001001", + "lbl" : "neuron projection bundle", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/CARO_0001010", + "lbl" : "organism or virus or viroid", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-07T12:58:06Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Melissa Haendel" } ] - }, - "type" : "PROPERTY", - "lbl" : "in register with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002029", + "id" : "http://purl.obolibrary.org/obo/CARO_0010000", + "lbl" : "multicellular anatomical structure", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.", - "xrefs" : [ "PMID:24138933", "Wikipedia:Infant_mortality" ] + "val" : "An anatomical structure that has more than one cell as a part." }, - "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-05-22T16:43:28Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "djs93" } ] - }, - "type" : "PROPERTY", - "lbl" : "has increased age-specific mortality rate" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0016004", + "id" : "http://purl.obolibrary.org/obo/CL_0000000", + "lbl" : "cell", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y.", - "xrefs" : [ ] + "val" : "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.", + "xrefs" : [ "CARO:mah" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7463-6306" + "comments" : [ "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)." ], + "xrefs" : [ { + "val" : "CALOHA:TS-2035" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ExO:0000083" + "val" : "FBbt:00007002" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-12-14T20:41:45Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has exposure medium" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0016001", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." + "val" : "FMA:68646" }, { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-11-05T17:30:14Z" + "val" : "GO:0005623" }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "KUPO:0000002" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/478" + "val" : "MESH:D002477" + }, { + "val" : "VHOG:0001533" + }, { + "val" : "WBbt:0004017" + }, { + "val" : "XAO:0003012" } ] - }, - "type" : "PROPERTY", - "lbl" : "has phenotype or disease" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0016002", + "id" : "http://purl.obolibrary.org/obo/CL_0000101", + "lbl" : "sensory neuron", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.", - "xrefs" : [ ] + "val" : "Any neuron having a sensory function; an afferent neuron conveying sensory impulses.", + "xrefs" : [ "ISBN:0721662544" ] }, - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/date", - "val" : "2021-11-05T17:30:44Z" + "xrefs" : [ { + "val" : "BTO:0001037" }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "http://orcid.org/0000-0002-7463-6306" + "val" : "FBbt:00005124" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/478" + "val" : "FMA:84649" + }, { + "val" : "MESH:D011984" + }, { + "val" : "WBbt:0005759" } ] - }, - "type" : "PROPERTY", - "lbl" : "has disease" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "id" : "http://purl.obolibrary.org/obo/CL_0000540", + "lbl" : "neuron", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence", - "xrefs" : [ ] + "val" : "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.", + "xrefs" : [ "MESH:D009474", "http://en.wikipedia.org/wiki/Neuron" ] }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this investigator role is a role of this person" + "comments" : [ "These cells are also reportedly CD4-negative and CD200-positive. 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Note that this relation is now removed from BFO2020." ], + "comments" : [ "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "environment" + } ], + "xrefs" : [ { + "val" : "EcoLexicon:environment" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "quality_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A quality inheres in its bearer at all times for which the quality exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is quality of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this red color is a quality of this apple" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2013-09-23T16:04:08Z" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01003004", + "lbl" : "derives from part of", "type" : "PROPERTY", - "lbl" : "quality of" + "meta" : { + "definition" : { + "val" : "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044456", + "id" : "http://purl.obolibrary.org/obo/GO_0003674", + "lbl" : "molecular_function", + "type" : "CLASS", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/go.owl" + "definition" : { + "val" : "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.", + "xrefs" : [ "GOC:pdt" ] + }, + "comments" : [ "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecular function" } ] - }, - "type" : "CLASS", - "lbl" : "synapse part" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "id" : "http://purl.obolibrary.org/obo/GO_0004842", + "lbl" : "ubiquitin-protein transferase activity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence", - "xrefs" : [ ] + "val" : "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.", + "xrefs" : [ "GOC:BioGRID", "GOC:jh2", "PMID:9635407" ] }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "anaphase-promoting complex activity", + "xrefs" : [ "GOC:dph", "GOC:tb" ] }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + "pred" : "hasNarrowSynonym", + "val" : "ubiquitin conjugating enzyme activity" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_function" + "pred" : "hasNarrowSynonym", + "val" : "ubiquitin ligase activity" + }, { + "pred" : "hasNarrowSynonym", + "val" : "ubiquitin protein ligase activity" + }, { + "pred" : "hasNarrowSynonym", + "val" : "ubiquitin protein-ligase activity" + }, { + "pred" : "hasNarrowSynonym", + "val" : "ubiquitin-conjugating enzyme activity" + }, { + "pred" : "hasRelatedSynonym", + "val" : "E2" + }, { + "pred" : "hasRelatedSynonym", + "val" : "E3" + } 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In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.", + "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "affects", - "xrefs" : [ ] + "pred" : "hasExactSynonym", + "val" : "cell nucleus" + }, { + "pred" : "hasNarrowSynonym", + "val" : "horsetail nucleus", + "xrefs" : [ "GOC:al", "GOC:mah", "GOC:vw", "PMID:15030757" ] } ], - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + "xrefs" : [ { + "val" : "NIF_Subcellular:sao1702920020" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + "val" : "Wikipedia:Cell_nucleus" } ] - }, - "type" : "PROPERTY", - "lbl" : "acts upstream of or within" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "id" : "http://purl.obolibrary.org/obo/GO_0008150", + "lbl" : "biological_process", + "type" : "CLASS", "meta" : { - "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). 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When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "biological process" + }, { + "pred" : "hasExactSynonym", + "val" : "physiological process" + }, { + "pred" : "hasRelatedSynonym", + "val" : "single organism process" }, { + "pred" : "hasRelatedSynonym", + "val" : "single-organism process" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Biological_process" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "jl" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-09-19T15:05:24Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly regulated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "id" : "http://purl.obolibrary.org/obo/GO_0016301", + "lbl" : "kinase activity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "val" : "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", + "xrefs" : [ "ISBN:0198506732" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:38Z" + "comments" : [ "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "phosphokinase activity" + } ], + "xrefs" : [ { + "val" : "Reactome:R-HSA-6788855" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "Reactome:R-HSA-6788867" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly negatively regulated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "id" : "http://purl.obolibrary.org/obo/GO_0019107", + "lbl" : "myristoyltransferase activity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", - "xrefs" : [ "GOC:dos" ] + "val" : "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.", + "xrefs" : [ "GOC:ai" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-17T13:52:47Z" + "xrefs" : [ { + "val" : "Reactome:R-HSA-141367" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "val" : "Reactome:R-HSA-162914" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly positively regulated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "id" : "http://purl.obolibrary.org/obo/IAO_0000078", + "lbl" : "curation status specification", "meta" : { - "definition" : { - "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", - "xrefs" : [ "GOC:dos" ] - }, - "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-09-22T14:14:36Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] - }, - "type" : "PROPERTY", - "lbl" : "has effector activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", "meta" : { - "definition" : { - "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "has biological role" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "lbl" : "obsolescence reason specification", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)", - "xrefs" : [ ] + "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." } - }, - "type" : "PROPERTY", - "lbl" : "has application role" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", "meta" : { - "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] - }, - "type" : "PROPERTY", - "lbl" : "has role" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl" : "OBO foundry unique label", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-07-20T17:11:08Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", "type" : "PROPERTY", - "lbl" : "transports" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "id" : "http://purl.obolibrary.org/obo/OGMS_0000031", + "lbl" : "disease", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)", - "xrefs" : [ ] + "val" : "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." } - }, - "type" : "PROPERTY", - "lbl" : "has chemical role" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence", - "xrefs" : [ ] + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this apple has quality this red color" + "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : = α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))", - "xrefs" : [ ] + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" } ] - }, - "type" : "PROPERTY", - "lbl" : "existence overlaps" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t", - "xrefs" : [ ] + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002494" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" } ] - }, - "type" : "PROPERTY", - "lbl" : "immediate transformation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002011", + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between a process that regulates a transport process and the entity transported by that process.", - "xrefs" : [ ] + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" } ] - }, - "type" : "PROPERTY", - "lbl" : "regulates transport of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of connecting branch of", - "xrefs" : [ ] + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", "type" : "PROPERTY", - "lbl" : "has connecting branch" + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A part of relation that applies only between occurrents.", - "xrefs" : [ ] + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" } - }, - "type" : "PROPERTY", - "lbl" : "occurrent part of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).", - "xrefs" : [ ] + "val" : "inverse of has disposition" }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "existence starts during or after" + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "id" : "http://purl.obolibrary.org/obo/RO_0000300", + "lbl" : "obsolete in neural circuit with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has developmental contribution from y iff x has some part z such that z develops from y", - "xrefs" : [ ] + "val" : "OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons." }, + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has developmental contribution from" + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "id" : "http://purl.obolibrary.org/obo/RO_0000301", + "lbl" : "obsolete upstream in neural circuit with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.", - "xrefs" : [ ] + "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "existence ends during or before" + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "id" : "http://purl.obolibrary.org/obo/RO_0000302", + "lbl" : "obsolete downstream in neural circuit with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.", - "xrefs" : [ ] + "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first." }, + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:30:46Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has regulatory component activity" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has developmental contribution from", - "xrefs" : [ ] + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this cell derives from this parent cell (cell division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this nucleus derives from this parent nucleus (nuclear division)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_from" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." } ] - }, - "type" : "PROPERTY", - "lbl" : "developmentally contributes to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.", - "xrefs" : [ ] + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "dos" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent cell derives into this cell (cell division)" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-05-24T09:31:01Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this parent nucleus derives into this nucleus (nuclear division)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "derives_into" } ] - }, - "type" : "PROPERTY", - "lbl" : "has negative regulatory component activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T", - "xrefs" : [ ] + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO:0001759" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is location of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my head is the location of my brain" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this cage is the location of this rat" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + "val" : "location_of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "developmentally induced by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "id" : "http://purl.obolibrary.org/obo/RO_0001018", + "lbl" : "contained in", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)", - "xrefs" : [ ] - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "exists during", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "contained in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "existence starts and ends during" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "id" : "http://purl.obolibrary.org/obo/RO_0001019", + "lbl" : "contains", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).", - "xrefs" : [ ] - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "contains" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "existence ends during" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).", - "xrefs" : [ ] + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", "type" : "PROPERTY", - "lbl" : "existence ends with" + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships", - "xrefs" : [ ] + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", "type" : "PROPERTY", - "lbl" : "transformation of" + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t.", - "xrefs" : [ ] + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "located in" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + "val" : "my brain is located in my head" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/2212" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this rat is located in this cage" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "located_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" } ] - }, - "type" : "PROPERTY", - "lbl" : "connecting branch of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "id" : "http://purl.obolibrary.org/obo/RO_0001900", + "lbl" : "temporal interpretation", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).", - "xrefs" : [ ] + "val" : "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" } ] - }, - "type" : "PROPERTY", - "lbl" : "regulates in other organism" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "id" : "http://purl.obolibrary.org/obo/RO_0001901", + "lbl" : "axiom holds for all times", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "## Elucidation\n\nThis is used when the statement/axiom is assumed to hold true 'eternally'\n\n## How to interpret (informal)\n\nFirst the "atemporal" FOL is derived from the OWL using the standard\ninterpretation. This axiom is temporalized by embedding the axiom\nwithin a for-all-times quantified sentence. The t argument is added to\nall instantiation predicates and predicates that use this relation.\n\n## Example\n\n Class: nucleus\n SubClassOf: part_of some cell\n\n forall t :\n forall n :\n instance_of(n,Nucleus,t)\n implies\n exists c :\n instance_of(c,Cell,t)\n part_of(n,c,t)\n\n## Notes\n\nThis interpretation is *not* the same as an at-all-times relation" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001902", + "lbl" : "relation has no temporal argument", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "## Elucidation\n\nThis is used when the first-order logic form of the relation is\nbinary, and takes no temporal argument.\n\n## Example:\n\n Class: limb\n SubClassOf: develops_from some lateral-plate-mesoderm\n\n forall t, t2:\n forall x :\n instance_of(x,Limb,t)\n implies\n exists y :\n instance_of(y,LPM,t2)\n develops_from(x,y)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.", - "xrefs" : [ ] + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" }, - "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note from NCEAS meeting: consider changing primary label" + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "coincident with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002009", + "id" : "http://purl.obolibrary.org/obo/RO_0002001", + "lbl" : "aligned with", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/description", - "val" : "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "cell expresses" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002004", + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).", - "xrefs" : [ ] + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_2D_boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "tracheates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "lbl" : "electrically_synapsed_to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).", - "xrefs" : [ ] + "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "existence starts during" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002246", - "meta" : { - "definition" : { - "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "under-expressed in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002005", - "meta" : { - "basicPropertyValues" : [ { + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { "pred" : "http://purl.org/spar/cito/citesAsAuthority", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" } ] - }, - "type" : "PROPERTY", - "lbl" : "innervated_by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "id" : "http://purl.obolibrary.org/obo/RO_0002004", + "lbl" : "tracheates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).", - "xrefs" : [ ] + "val" : "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0002-7073-9172" } ] - }, - "type" : "PROPERTY", - "lbl" : "existence starts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "id" : "http://purl.obolibrary.org/obo/RO_0002005", + "lbl" : "innervated_by", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.", - "xrefs" : [ ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "has active pharmaceutical ingredient", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "has active substance", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "has active ingredient" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "has synaptic terminal of" + } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000", - "xrefs" : [ ] + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" }, "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], @@ -1290,2203 +1862,2117 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" } ] - }, - "type" : "PROPERTY", - "lbl" : "bounding layer of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002249", - "meta" : { - "definition" : { - "val" : "inverse of has active ingredient", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "lbl" : "coincident with", "type" : "PROPERTY", - "lbl" : "active ingredient in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002000", "meta" : { "definition" : { - "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity", - "xrefs" : [ ] + "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." }, + "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the surface of my skin is a 2D boundary of my body" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is 2D boundary of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is boundary of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "boundary of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "2D_boundary_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "val" : "Note from NCEAS meeting: consider changing primary label" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "surface of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" } ] - }, - "type" : "PROPERTY", - "lbl" : "2D boundary of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002242", - "meta" : { - "definition" : { - "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ExO:0000055" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002009", + "lbl" : "cell expresses", "type" : "PROPERTY", - "lbl" : "has exposure route" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002484", "meta" : { "definition" : { - "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "curator guidance link" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002485", - "meta" : { + "val" : "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See notes for inverse relation" + "pred" : "http://purl.org/dc/terms/description", + "val" : "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" } ] - }, - "type" : "PROPERTY", - "lbl" : "receives input from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002001", + "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "lbl" : "regulates in other organism", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] - }, - "type" : "PROPERTY", - "lbl" : "aligned with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "id" : "http://purl.obolibrary.org/obo/RO_0002011", + "lbl" : "regulates transport of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target.", - "xrefs" : [ ] + "val" : "A relationship that holds between a process that regulates a transport process and the entity transported by that process." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "lbl" : "occurrent part of", "type" : "PROPERTY", - "lbl" : "has exposure transport path" + "meta" : { + "definition" : { + "val" : "A part of relation that applies only between occurrents." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity", - "xrefs" : [ ] + "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_2D_boundary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has 2D boundary the surface of my skin" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has boundary" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has 2D boundary" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "sends output to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Any relationship between an exposure event or process and any other entity.", - "xrefs" : [ ] + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." }, + "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "related via exposure to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "lbl" : "has necessary component activity", + "type" : "PROPERTY", "meta" : { + "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "relation between physical entity and a process or stage" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions.", - "xrefs" : [ ] - }, + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:44:33Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "electrically_synapsed_to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002245", - "meta" : { - "definition" : { - "val" : "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", "type" : "PROPERTY", - "lbl" : "over-expressed in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002480", "meta" : { "definition" : { - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y", - "xrefs" : [ ] + "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Axiomatization to GO to be added later" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "ubiquitinates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002481", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "lbl" : "has ligand", "type" : "PROPERTY", - "lbl" : "is kinase activity" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002240", "meta" : { "definition" : { - "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.", - "xrefs" : [ ] + "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ExO:0000001" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-19T17:30:36Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has exposure receptor" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002482", + "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "lbl" : "transports", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:11:08Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "is ubiquitination" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.", - "xrefs" : [ ] + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "ExO:0000000" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has exposure stressor" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002483", + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", "type" : "PROPERTY", - "lbl" : "inherited annotation property" + "meta" : { + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000059", + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.", - "xrefs" : [ ] + "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", + "xrefs" : [ "GOC:dos" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:38Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "concretizes" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000058", + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.", - "xrefs" : [ ] + "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "is concretized as" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process", - "xrefs" : [ ] + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this process has participant this input material (or this output material)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this blood coagulation has participant this blood clot" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_participant" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this investigation has participant this investigator" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has participant" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has participant" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002235", - "meta" : { - "definition" : { - "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", "type" : "PROPERTY", - "lbl" : "stem parasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002477", "meta" : { "definition" : { - "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism", - "xrefs" : [ ] + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "child nucleus of in hermaphrodite" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "id" : "http://purl.obolibrary.org/obo/RO_0002029", + "lbl" : "has increased age-specific mortality rate", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A child nucleus relationship in which the cells are part of a male organism", - "xrefs" : [ ] + "val" : "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.", + "xrefs" : [ "PMID:24138933", "Wikipedia:Infant_mortality" ] }, + "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T16:43:28Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "child nucleus of in male" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002236", - "meta" : { - "definition" : { - "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", "type" : "PROPERTY", - "lbl" : "root parasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002479", "meta" : { - "definition" : { - "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.", - "xrefs" : [ ] - }, + "comments" : [ "Primitive instance level timing relation between events" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" } ] - }, - "type" : "PROPERTY", - "lbl" : "has part that occurs in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002237", - "meta" : { - "definition" : { - "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", "type" : "PROPERTY", - "lbl" : "hemiparasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002238", "meta" : { - "definition" : { - "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys.", - "xrefs" : [ ] - }, + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "has component participant" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y", - "xrefs" : [ ] - }, + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts with process that occurs in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "has start location" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.", - "xrefs" : [ ] - }, + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "composed primarily of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.", - "xrefs" : [ ] - }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this red color is a characteristic of this apple" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this fragility is a characteristic of this vase" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "inheres in" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "val" : "di" } ] - }, - "type" : "PROPERTY", - "lbl" : "characteristic of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y", - "xrefs" : [ ] - }, + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends with process that occurs in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "has end location" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002474", - "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", "type" : "PROPERTY", - "lbl" : "dispositional interpretation" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002233", "meta" : { - "definition" : { - "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "consumes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "starts_at_end_of" } ] - }, - "type" : "PROPERTY", - "lbl" : "has input" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002475", + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "lbl" : "during which starts", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other.", - "xrefs" : [ ] - }, + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "shares no connection with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "has no connections with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "produces" + "val" : "David Osumi-Sutherland" } ] - }, - "type" : "PROPERTY", - "lbl" : "has output" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d", - "xrefs" : [ ] - }, + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "David Osumi-Sutherland" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" } ] - }, - "type" : "PROPERTY", - "lbl" : "child nucleus of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process", - "xrefs" : [ ] - }, + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this investigator participates in this investigation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this input material (or this output material) participates in this process" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this blood clot participates in this blood coagulation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "participates in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "participates_in" + "val" : "io" } ] - }, - "type" : "PROPERTY", - "lbl" : "participates in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is subject of eating interaction with" + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" } ] - }, - "type" : "PROPERTY", - "lbl" : "eats" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "eaten by" + "val" : "o" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is target of eating interaction with" + "val" : "overlaps" } ] - }, - "type" : "PROPERTY", - "lbl" : "is eaten by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002472", + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b.", - "xrefs" : [ ] + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "is evidence for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of", - "xrefs" : [ ] + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this apple is bearer of this red color" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this vase is bearer of this fragility" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is bearer of" + "val" : "fasciculates with" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "bearer_of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "bearer of" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "has characteristic" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", - "xrefs" : [ ] + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "ends with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002228", - "meta" : { - "definition" : { - "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", "type" : "PROPERTY", - "lbl" : "facultative parasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002229", "meta" : { "definition" : { - "val" : "inverse of ends with", - "xrefs" : [ ] + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "ends" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. 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These properties exist as helper properties that are used to support OWL reasoning." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "helper property (not for use in curation)" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "id" : "http://purl.obolibrary.org/obo/RO_0002115", + "lbl" : "synapsed_by_via_type_III_bouton", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of starts with", - "xrefs" : [ ] + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type III bouton.\n" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "starts" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003311", - "meta" : { - "definition" : { - "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002120", + "lbl" : "synapsed to", "type" : "PROPERTY", - "lbl" : "condition exacerbated by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002465", "meta" : { + "definition" : { + "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " + }, + "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is symbiosis" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002460", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "has vector" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002461", + "id" : "http://purl.obolibrary.org/obo/RO_0002121", + "lbl" : "dendrite synapsed in", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n\t" + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n\t and some (\n\t http://purl.obolibrary.org/obo/GO_0042734 and some (\n\t and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "partner in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "id" : "http://purl.obolibrary.org/obo/RO_0002130", + "lbl" : "has synaptic terminal in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.", - "xrefs" : [ ] + "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, - "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preventative for condition" - } ] - }, - "type" : "PROPERTY", - "lbl" : "ameliorates condition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002459", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" + "val" : "has synapse in" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Anopheles is a vector for Plasmodium" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "is vector for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002217", + "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "lbl" : "overlaps", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role", - "xrefs" : [ ] + "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, - "comments" : [ "Obsoleted as the inverse property was obsoleted." ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "agent in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0002608" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete actively participates in" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002218", + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y", - "xrefs" : [ ] + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has agent" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0002500" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete has active participant" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003306", - "meta" : { - "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contributes to penetrance of condition" + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "contributes to frequency of condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "id" : "http://purl.obolibrary.org/obo/RO_0002134", + "lbl" : "innervates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x", - "xrefs" : [ ] + "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that ( some ( that some Y?)))" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] - }, - "type" : "PROPERTY", - "lbl" : "surrounded by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003309", - "meta" : { - "definition" : { - "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "exacerbates condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003308", - "meta" : { - "definition" : { - "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", "type" : "PROPERTY", - "lbl" : "correlated with condition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", "meta" : { "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.", - "xrefs" : [ ] + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "positively regulates (process to process)" - } ] - }, - "type" : "PROPERTY", - "lbl" : "positively regulates" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003303", - "meta" : { - "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", "type" : "PROPERTY", - "lbl" : "causes condition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002455", "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is subject of pollination interaction with" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/pollinates" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Bees pollinate Flowers" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "pollinates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "lbl" : "derived by descent from", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has polinator" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is target of pollination interaction with" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/hasPollinator" + "val" : "ancestral_stucture_of" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "evolutionarily_descended_from" } ] - }, - "type" : "PROPERTY", - "lbl" : "pollinated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "lbl" : "has derived by descendant", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.", - "xrefs" : [ ] + "val" : "inverse of derived by descent from" }, - "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] - }, - "type" : "PROPERTY", - "lbl" : "causes or contributes to condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002214", + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation.", - "xrefs" : [ ] + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, + "comments" : [ "VBO calls this homologous_to" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO: add homeomorphy axiom" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" } ] - }, - "type" : "PROPERTY", - "lbl" : "has prototype" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "lbl" : "serially homologous to", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] - }, - "type" : "PROPERTY", - "lbl" : "acquires nutrients from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. ", - "xrefs" : [ ] + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "capable of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.", - "xrefs" : [ ] + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contributes to expressivity of condition" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "contributes to severity of condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003304", - "meta" : { - "definition" : { - "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", "type" : "PROPERTY", - "lbl" : "contributes to condition" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002458", "meta" : { "definition" : { - "val" : "inverse of preys on", - "xrefs" : [ ] + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/HasPredator" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9227-417X" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is target of predation interaction with" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has predator" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "preyed upon by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.", - "xrefs" : [ ] + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" } ] - }, - "type" : "PROPERTY", - "lbl" : "capable of part of" - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0001010", - "type" : "CLASS", - "lbl" : "organism or virus or viroid" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002451", + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between a disease and organism", - "xrefs" : [ ] + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "all dengue disease transmitted by some mosquito" + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Add domain and range constraints" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] - }, - "type" : "PROPERTY", - "lbl" : "transmitted by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "id" : "http://purl.obolibrary.org/obo/RO_0002171", + "lbl" : "mutually spatially disjoint with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of directly develops from", - "xrefs" : [ ] + "val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "developmental precursor of" + "val" : "non-overlapping with" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no parts with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX owl: \nPREFIX part_of: \nPREFIX mutually_spatially_disjoint_with: \nCONSTRUCT {\n part_of: a owl:ObjectProperty .\n [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?x ;\n owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?y\n ]\n ]\n}\nWHERE {\n ?x mutually_spatially_disjoint_with: ?y .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/RO_0002163" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly develops into" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002452", + "id" : "http://purl.obolibrary.org/obo/RO_0002172", + "lbl" : "taxonomic class assertion", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between a disease or an organism and a phenotype", - "xrefs" : [ ] + "val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002173", + "lbl" : "ambiguous for taxon", "type" : "PROPERTY", - "lbl" : "has symptom" + "meta" : { + "definition" : { + "val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "id" : "http://purl.obolibrary.org/obo/RO_0002174", + "lbl" : "dubious for taxon", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.", - "xrefs" : [ ] + "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" + }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7476-6306" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-3837-8864" + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002453", + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", "type" : "PROPERTY", - "lbl" : "host of" + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity.", - "xrefs" : [ ] + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "comments" : [ "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-1048-5019" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is used to study" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" } ] - }, - "type" : "PROPERTY", - "lbl" : "has role in modeling" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000402", - "type" : "CLASS", - "lbl" : "branched" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y", - "xrefs" : [ ] + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/hasHost" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" } ] - }, - "type" : "PROPERTY", - "lbl" : "has host" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.", - "xrefs" : [ ] + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ] - }, - "type" : "PROPERTY", - "lbl" : "negatively regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.", - "xrefs" : [ ] + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "molecularly increases activity of", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly activates" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly positively regulates activity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.", - "xrefs" : [ ] + "val" : "inverse of has phenotype" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "molecularly controls", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly regulates activity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process", - "xrefs" : [ ] + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, + "comments" : [ "This is the transitive form of the develops from relation" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" } ] - }, - "type" : "PROPERTY", - "lbl" : "expressed in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.", - "xrefs" : [ ] + "val" : "inverse of develops from" }, - "comments" : [ "TODO - add child relations from DOS" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "has developmental precursor", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly develops from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "id" : "http://purl.obolibrary.org/obo/RO_0002204", + "lbl" : "gene product of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.", - "xrefs" : [ ] + "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "molecularly decreases activity of", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly negatively regulates activity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002208", - "meta" : { - "definition" : { - "val" : "A parasite that kills or sterilizes its host", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "lbl" : "has gene product", "type" : "PROPERTY", - "lbl" : "parasitoid of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002209", "meta" : { "definition" : { - "val" : "inverse of parasitoid of", - "xrefs" : [ ] + "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "has parasitoid" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002444", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "direct parasite of", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Pediculus humanus capitis parasite of human" + "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "parasitizes" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/parasitizes" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "parasite of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y", - "xrefs" : [ ] + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" }, - "comments" : [ "This is the transitive form of the develops from relation" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "develops from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of develops from", - "xrefs" : [ ] + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", "type" : "PROPERTY", - "lbl" : "develops into" + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002445", + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "directly parasitized by", - "xrefs" : [ ] - } ], + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has parasite" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/hasParasite" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "parasitised by" + "val" : "developmental precursor of" } ] - }, - "type" : "PROPERTY", - "lbl" : "parasitized by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002204", + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"", - "xrefs" : [ ] + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" } ] - }, - "type" : "PROPERTY", - "lbl" : "gene product of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored.", - "xrefs" : [ ] + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "semibiotically interacts with", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Porifiera attaches to substrate" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] - }, - "type" : "PROPERTY", - "lbl" : "participates in a abiotic-biotic interaction with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y", - "xrefs" : [ ] + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] - }, - "type" : "PROPERTY", - "lbl" : "has gene product" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002447", + "id" : "http://purl.obolibrary.org/obo/RO_0002214", + "lbl" : "has prototype", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Axiomatization to GO to be added later" + "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "phosphorylates" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", "type" : "PROPERTY", - "lbl" : "editor note" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000117", "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." } ] - }, - "type" : "PROPERTY", - "lbl" : "term editor" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000114", + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", "type" : "PROPERTY", - "lbl" : "has curation status" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] - }, - "type" : "PROPERTY", - "lbl" : "definition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018002", + "id" : "http://purl.obolibrary.org/obo/RO_0002217", + "lbl" : "obsolete actively participates in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input", - "xrefs" : [ ] + "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" }, + "comments" : [ "Obsoleted as the inverse property was obsoleted." ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/conformsTo", - "val" : "http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - }, - "type" : "PROPERTY", - "lbl" : "myristoylates" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "agent in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002608" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000112", + "id" : "http://purl.obolibrary.org/obo/RO_0002218", + "lbl" : "obsolete has active participant", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - } ] - }, - "type" : "PROPERTY", - "lbl" : "example of usage" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has agent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002500" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018001", + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Helper relation for OWL definition of RO:0018002 myristoylates", - "xrefs" : [ ] + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "is myristoyltransferase activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000111", + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", "type" : "PROPERTY", - "lbl" : "editor preferred term" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018003", "meta" : { "definition" : { - "val" : "inverse of myristoylates", - "xrefs" : [ ] + "val" : "x adjacent to y if and only if x and y share a boundary." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "myristoylated by" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000118", + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "alternative term" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000119", + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" } ] - }, - "type" : "PROPERTY", - "lbl" : "definition source" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002440", + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A biotic interaction in which the two organisms live together in more or less intimate association.", - "xrefs" : [ ] + "val" : "inverse of starts with" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + "val" : "Allen" } ] - }, - "type" : "PROPERTY", - "lbl" : "symbiotically interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002441", + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO).", - "xrefs" : [ ] + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" } ] - }, - "type" : "PROPERTY", - "lbl" : "commensually interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).", - "xrefs" : [ ] + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" @@ -3494,15274 +3980,14148 @@ "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has phenotype" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002442", + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO).", - "xrefs" : [ ] + "val" : "x develops_in y if x is located in y whilst x is developing" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", "type" : "PROPERTY", - "lbl" : "mutualistically interacts with" + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has phenotype", - "xrefs" : [ ] + "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" } ] - }, - "type" : "PROPERTY", - "lbl" : "phenotype of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).", - "xrefs" : [ ] + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "finished by" } ] - }, - "type" : "PROPERTY", - "lbl" : "interacts with via parasite-host interaction" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002437", + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.", - "xrefs" : [ ] + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/interactsWith" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "interacts with on organism level" + "val" : "starts with process that occurs in" } ] - }, - "type" : "PROPERTY", - "lbl" : "biotically interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002438", + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship in which the partners are related via a feeding relationship.", - "xrefs" : [ ] + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" } ] - }, - "type" : "PROPERTY", - "lbl" : "trophically interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members", - "xrefs" : [ ] + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Baleen whale preys on krill" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/preysUpon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preys upon" + "val" : "consumes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is subject of predation interaction with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7134-3324" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-3138-4118" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.inaturalist.org/observations/2942824" + "val" : "produces" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", "type" : "PROPERTY", - "lbl" : "preys on" + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", "type" : "PROPERTY", - "lbl" : "contributes to morphology of" + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.", - "xrefs" : [ ] + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "in pairwise interaction with", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0914" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + "val" : "https://orcid.org/0000-0001-9625-1899" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Considering relabeling as 'pairwise interacts with'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." } ] - }, - "type" : "PROPERTY", - "lbl" : "interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002435", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0208" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ECO_0000316" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", "type" : "PROPERTY", - "lbl" : "genetically interacts with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002436", "meta" : { "definition" : { - "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.", - "xrefs" : [ ] + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" } ] - }, - "type" : "PROPERTY", - "lbl" : "molecularly interacts with" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "pending final vetting" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" } ] - }, - "type" : "INDIVIDUAL", - "lbl" : "ready for release" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p", - "xrefs" : [ ] + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" } ] - }, - "type" : "PROPERTY", - "lbl" : "involved in negative regulation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p", - "xrefs" : [ ] + "val" : "Any relationship between an exposure event or process and any other entity." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "OWL does not allow defining object properties via a Union" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002245", + "lbl" : "over-expressed in", "type" : "PROPERTY", - "lbl" : "involved in or involved in regulation of" + "meta" : { + "definition" : { + "val" : "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "id" : "http://purl.obolibrary.org/obo/RO_0002246", + "lbl" : "under-expressed in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", - "xrefs" : [ "GOC:cjm", "GOC:dos" ] + "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." }, - "comments" : [ "" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "enables activity in", - "xrefs" : [ ] + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes activity in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A protein that enables activity in a cytosol." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", "type" : "PROPERTY", - "lbl" : "is active in" + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] - }, - "type" : "PROPERTY", - "lbl" : "differs in attribute" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of causally upstream of or within", - "xrefs" : [ ] + "val" : "inverse of connecting branch of" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally downstream of or within" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p", - "xrefs" : [ ] + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "involved in regulation of" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0008150", - "type" : "CLASS", - "lbl" : "biological_process" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p", - "xrefs" : [ ] + "val" : "inverse of has developmental contribution from" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "involved in positive regulation of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002422", - "meta" : { - "definition" : { - "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "logical macro assertion on an object property" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", "type" : "PROPERTY", - "lbl" : "logical macro assertion on an annotation property" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002424", "meta" : { - "comments" : [ "This is an exploratory relation" ], + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0001-9114-8737" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "false" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" - } ] - }, - "type" : "PROPERTY", - "lbl" : "differs in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002425", - "meta" : { - "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "differs in attribute of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018028", - "meta" : { - "definition" : { - "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "https://orcid.org/0000-0003-4423-4370" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://www.wikidata.org/wiki/Property:P9275" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" } ] - }, - "type" : "PROPERTY", - "lbl" : "is inverse agonist of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018027", + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor", - "xrefs" : [ ] + "val" : "Inverse of developmentally induced by" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "https://orcid.org/0000-0003-4423-4370" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://www.wikidata.org/wiki/Property:P3772" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is agonist of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0018029", + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level", - "xrefs" : [ ] + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "https://orcid.org/0000-0003-4423-4370" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://www.wikidata.org/wiki/Property:P3773" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] - }, - "type" : "PROPERTY", - "lbl" : "is antagonist of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002420", + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "lbl" : "defined by inverse", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A logical macro assertion whose domain is an IRI for a class", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" - } ] - }, - "type" : "PROPERTY", - "lbl" : "logical macro assertion on a class" + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002421", + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A logical macro assertion whose domain is an IRI for a property", - "xrefs" : [ ] + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" } - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", "type" : "PROPERTY", - "lbl" : "logical macro assertion on a property" + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002416", + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.", - "xrefs" : [ ] + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] - }, - "type" : "PROPERTY", - "lbl" : "logical macro assertion" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.", - "xrefs" : [ ] + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "affects", - "xrefs" : [ ] + "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "influences (processual)" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally upstream of or within" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.", - "xrefs" : [ ] + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally upstream of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.", - "xrefs" : [ ] + "val" : "Inverse of developmentally preceded by" }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" } ] - }, - "type" : "PROPERTY", - "lbl" : "immediately causally upstream of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly provides input for (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly provides input for" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "provides input for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "id" : "http://purl.obolibrary.org/obo/RO_0002291", + "lbl" : "ubiquitously expressed in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "transitive form of directly_provides_input_for", - "xrefs" : [ ] + "val" : "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "transitively provides input for (process to process)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" } ] - }, - "type" : "PROPERTY", - "lbl" : "transitively provides input for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002419", - "meta" : { - "definition" : { - "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", "type" : "PROPERTY", - "lbl" : "annotation property cardinality" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002410", "meta" : { "definition" : { - "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + "val" : "Inverse of 'expressed in'" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "id" : "http://purl.obolibrary.org/obo/RO_0002293", + "lbl" : "ubiquitously expresses", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of upstream of", - "xrefs" : [ ] + "val" : "inverse of ubiquiotously expressed in" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally downstream of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" } ] - }, - "type" : "PROPERTY", - "lbl" : "immediately causally downstream of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002406", - "meta" : { - "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0002629" - } ], - "deprecated" : true - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", "type" : "PROPERTY", - "lbl" : "obsolete directly activates" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002407", "meta" : { "definition" : { - "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.", - "xrefs" : [ ] + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002213" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" } ] - }, - "type" : "PROPERTY", - "lbl" : "indirectly positively regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.", - "xrefs" : [ ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly consumes" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" } ] - }, - "type" : "PROPERTY", - "lbl" : "has direct input" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002401", + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete has indirect input" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002402", + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. ", - "xrefs" : [ ] + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly produces" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "translation SubClassOf has_direct_output some protein" + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete has direct output" + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002403", + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete has indirect output" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002408", + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", "meta" : { - "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0002630" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete directly inhibits" + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.", - "xrefs" : [ ] + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002212" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0002-4366-3088" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" + "val" : "adapted for living in" } ] - }, - "type" : "PROPERTY", - "lbl" : "indirectly negatively regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002640", + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A sub-relation of endoparasite-of in which the parasite inhabits host cells.", - "xrefs" : [ ] + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "intracellular endoparasite of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002641", + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of intracellular endoparasite of", - "xrefs" : [ ] + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "has intracellular endoparasite" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002635", - "type" : "PROPERTY", - "lbl" : "has endoparasite" + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002636", - "meta" : { - "definition" : { - "val" : "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", "type" : "PROPERTY", - "lbl" : "mesoparasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002637", "meta" : { "definition" : { - "val" : "inverse of mesoparasite of", - "xrefs" : [ ] + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "has mesoparasite" + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002638", + "id" : "http://purl.obolibrary.org/obo/RO_0002310", + "lbl" : "exposure event or process", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells.", - "xrefs" : [ ] + "val" : "A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:55:39Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/pull/173" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002312", + "lbl" : "evolutionary variant of", "type" : "PROPERTY", - "lbl" : "intercellular endoparasite of" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002632", + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host", - "xrefs" : [ ] + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" } ] - }, - "type" : "PROPERTY", - "lbl" : "ectoparasite of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002633", + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of ectoparasite of", - "xrefs" : [ ] + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "has ectoparasite" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002634", - "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "lives inside of", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] - }, - "type" : "PROPERTY", - "lbl" : "endoparasite of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002639", - "meta" : { - "definition" : { - "val" : "inverse of intercellular endoparasite of", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "has intercellular endoparasite" + } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", "type" : "PROPERTY", - "lbl" : "database_cross_reference" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002630", "meta" : { "definition" : { - "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.", - "xrefs" : [ ] + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly negatively regulates (process to process)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "val" : "GOC:mtg_berkeley_2013" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly negatively regulates" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002624", - "type" : "PROPERTY", - "lbl" : "lays eggs in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002625", + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", "type" : "PROPERTY", - "lbl" : "has eggs laid in by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002626", "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://github.com/jhpoelen/eol-globi-data/issues/143" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." } ] - }, - "type" : "PROPERTY", - "lbl" : "kills" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002627", - "type" : "PROPERTY", - "lbl" : "is killed by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002622", + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", "type" : "PROPERTY", - "lbl" : "visits flowers of" + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002623", + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", "type" : "PROPERTY", - "lbl" : "has flowers visited by" - }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:05:18Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" } ] - }, - "type" : "PROPERTY", - "lbl" : "valid_for_go_gp2term" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.", - "xrefs" : [ ] + "val" : "A mereological relationship or a topological relationship" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly positively regulates (process to process)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly positively regulates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002613", + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom", - "xrefs" : [ ] + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" } ] - }, - "type" : "PROPERTY", - "lbl" : "axiom contradicted by evidence" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002614", + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence.", - "xrefs" : [ ] + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." }, - "comments" : [ "In the Gene Ontology association model, this corresponds to the With/From field" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" } ] - }, - "type" : "PROPERTY", - "lbl" : "is evidence with support from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002615", - "meta" : { - "definition" : { - "val" : "Inverse of is-model-of", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", "type" : "PROPERTY", - "lbl" : "has model" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002616", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " } ] - }, - "type" : "PROPERTY", - "lbl" : "related via evidence or inference to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002610", + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.", - "xrefs" : [ ] + "val" : "c enables p iff c is capable of p and c acts to execute p." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Groups both positive and negative correlation" + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." } ] - }, - "type" : "PROPERTY", - "lbl" : "correlated with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002611", + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", "type" : "PROPERTY", - "lbl" : "evidential logical macro assertion on an axiom" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002612", "meta" : { "definition" : { - "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom", - "xrefs" : [ ] + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" } ] - }, - "type" : "PROPERTY", - "lbl" : "axiom has evidence" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000589", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", "type" : "PROPERTY", - "lbl" : "OBO foundry unique label" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002617", "meta" : { "definition" : { - "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent.", - "xrefs" : [ ] + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" } ] - }, - "type" : "PROPERTY", - "lbl" : "is representative IRI for equivalence set" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002618", + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/74" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" } ] - }, - "type" : "PROPERTY", - "lbl" : "visits" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002619", + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", "type" : "PROPERTY", - "lbl" : "visited by" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0003674", "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "molecular process" - } ] - }, - "type" : "CLASS", - "lbl" : "molecular_function" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000028", - "meta" : { - "definition" : { - "val" : "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000028", "ISBN:978-0674639416" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heterochrony", - "xrefs" : [ ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "hasExactSynonym", - "val" : "heterochronous homologous to", - "xrefs" : [ ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000028" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" } ] - }, - "type" : "PROPERTY", - "lbl" : "in heterochronous homology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000029", + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.", - "xrefs" : [ "http://en.wikipedia.org/wiki/Pedomorphosis", "http://purl.obolibrary.org/obo/HOM_0000029", "ISBN:978-0674639416" ] + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "juvenification", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "pedomorphosis", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000029" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" } ] - }, - "type" : "PROPERTY", - "lbl" : "in paedomorphorsis relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000026", + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.", - "xrefs" : [ "http://dx.doi.org/10.1006/scdb.1999.0338", "http://dx.doi.org/10.1038/nrg2099", "http://purl.obolibrary.org/obo/HOM_0000026" ] + "val" : "inverse of enables" }, - "comments" : [ "The converse of pro-orthologous." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "semi-orthologous to", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000026" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "in semi-orthology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000027", + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Iterative homology that involves structures arranged along the main body axis.", - "xrefs" : [ "http://dx.doi.org/10.1146/annurev.es.20.110189.000411", "http://purl.obolibrary.org/obo/HOM_0000027" ] + "val" : "inverse of regulates" }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "homonomy", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "serial homologous to", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000027" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" } ] - }, - "type" : "PROPERTY", - "lbl" : "in serial homology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000302", + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first.", - "xrefs" : [ ] + "val" : "inverse of negatively regulates" }, - "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete downstream in neural circuit with" + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000031", + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.", - "xrefs" : [ "http://en.wikipedia.org/wiki/Progenesis", "http://purl.obolibrary.org/obo/HOM_0000031", "ISBN:978-0674639416" ] + "val" : "inverse of positively regulates" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000031" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "in progenesis relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000301", + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first.", - "xrefs" : [ ] + "val" : "A relationship that holds via some process of localization" }, - "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - } ], - "deprecated" : true - }, - "type" : "PROPERTY", - "lbl" : "obsolete upstream in neural circuit with" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000032", + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paedomorphosis that is produced by a retardation of somatic development.", - "xrefs" : [ "http://en.wikipedia.org/wiki/Neoteny", "http://purl.obolibrary.org/obo/HOM_0000032", "ISBN:978-0674639416" ] + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "juvenilization", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "neotenous to", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000032" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "in neoteny relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000300", + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.", - "xrefs" : [ ] + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." }, - 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" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "1 to 1 orthologous to", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "1:1 orthology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "one-to-one orthology", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000020" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "in 1 to 1 orthology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000024", + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paralogy that results from a duplication preceding a given speciation event.", - "xrefs" : [ "http://dx.doi.org/10.1146/annurev.genet.39.073003.114725", "http://purl.obolibrary.org/obo/HOM_0000024" ] + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "alloparalogy", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "outparalogy", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "out-paralogous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000024" + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", "type" : "PROPERTY", - "lbl" : "in out-paralogy relationship with" + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000025", + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.", - "xrefs" : [ "http://dx.doi.org/10.1006/scdb.1999.0338", "http://dx.doi.org/10.1038/nrg2099", "http://purl.obolibrary.org/obo/HOM_0000025" ] + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. 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It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000006" + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" } ] - }, - "type" : "PROPERTY", - "lbl" : "in structural homology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000007", + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Homology that is defined by common descent.", - "xrefs" : [ "http://dx.doi.org/10.1016/S0169-5347(97)01125-7", "http://purl.obolibrary.org/obo/HOM_0000007", "ISBN:0123195837" ] + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues." ], - "xrefs" : [ { - "val" : "ECO:0000075" - } ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "homocracous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000003" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "in homocracy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000000", "BGEE:curator" ] + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" }, - "xrefs" : [ { - "val" : "ECO:0000041" - }, { - "val" : "SO:similar_to" - } ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "resemblance", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "sameness", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "similar to", - "xrefs" : [ ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "correspondence", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO: Add homeomorphy axiom" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000000" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "in similarity relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000001", + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Similarity that results from common evolutionary origin.", - "xrefs" : [ "http://dx.doi.org/10.1002/bies.950180611", "http://dx.doi.org/10.1002/jmor.1051730307", "http://dx.doi.org/10.1007/BF02814480", "http://purl.obolibrary.org/obo/HOM_0000001" ] + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." }, - "comments" : [ "This broad definition encompasses all the working definitions proposed so far in the literature." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "homologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000001" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002401", + "lbl" : "obsolete has indirect input", "type" : "PROPERTY", - "lbl" : "in homology relationship with" + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000075", + "id" : "http://purl.obolibrary.org/obo/RO_0002402", + "lbl" : "obsolete has direct output", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms.", - "xrefs" : [ "http://dx.doi.org/10.1101/gr.1774904", "http://purl.obolibrary.org/obo/HOM_0000075" ] + "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "regulogous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "translation SubClassOf has_direct_output some protein" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000075" - } ] - }, + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly produces" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002403", + "lbl" : "obsolete has indirect output", "type" : "PROPERTY", - "lbl" : "in regulogy relationship with" + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000073", + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Synology that results from allopolyploidy.", - "xrefs" : [ "http://dx.doi.org/10.1073/pnas.0505156102", "http://purl.obolibrary.org/obo/HOM_0000073" ] + "val" : "inverse of upstream of" }, - "comments" : [ "On a long term, it is hard to distinguish allopolyploidy from whole genome duplication." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "homoeologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000073" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002406", + "lbl" : "obsolete directly activates", "type" : "PROPERTY", - "lbl" : "in homoeology relationship with" + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002629" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000074", + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure.", - "xrefs" : [ "http://dx.doi.org/10.1007/s10441-007-9023-8", "http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x", "http://purl.obolibrary.org/obo/HOM_0000074" ] + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "axis paramorphism", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000074" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002408", + "lbl" : "obsolete directly inhibits", "type" : "PROPERTY", - "lbl" : "in paramorphism relationship with" + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002630" + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000071", + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Structural homology that involves structures with the same or similar relative positions.", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814484", "http://dx.doi.org/10.1007/BF02814485", "http://purl.obolibrary.org/obo/HOM_0000071", "ISBN:0123195837" ] + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, - "comments" : [ "Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "homotopous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000071" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" } ] - }, - "type" : "PROPERTY", - "lbl" : "in homotopy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000072", + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Biological homology that involves an ectopic structure and the normally positioned structure.", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814485", "http://dx.doi.org/10.1016/j.cell.2008.06.030", "http://purl.obolibrary.org/obo/HOM_0000072" ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "heterotopy", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000072" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] - }, - "type" : "PROPERTY", - "lbl" : "in homeosis relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000065", + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Similarity that is characterized by interchangeability in function.", - "xrefs" : [ "http://dx.doi.org/10.1007/BF02814484", "http://dx.doi.org/10.1038/415741a", "http://purl.obolibrary.org/obo/HOM_0000065" ] + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "functional similarity", - "xrefs" : [ ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000065" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "in functional equivalence relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000062", + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Historical homology that involves functional equivalent genes with retention of the ancestral function.", - "xrefs" : [ "http://dx.doi.org/10.1093/nar/gkl1043", "http://purl.obolibrary.org/obo/HOM_0000062" ] + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." }, - "comments" : [ "This may include examples of orthology, paralogy and xenology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "equivalogous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000062" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" } ] - }, - "type" : "PROPERTY", - "lbl" : "in equivalogy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000063", + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Historical homology that involves orthologous pairs of interacting molecules in different organisms.", - "xrefs" : [ "http://dx.doi.org/10.1101/gr.1774904", "http://dx.doi.org/10.1126/science.287.5450.116", "http://purl.obolibrary.org/obo/HOM_0000063" ] + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "interologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000063" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" } ] - }, - "type" : "PROPERTY", - "lbl" : "in interology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000068", + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000068", "http://www.ncbi.nlm.nih.gov/pubmed/3065587" ] + "val" : "transitive form of directly_provides_input_for" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "multiple xenology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "duplicate xenology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "paraxenologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000068" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" } ] - }, - "type" : "PROPERTY", - "lbl" : "in paraxenology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000069", + "id" : "http://purl.obolibrary.org/obo/RO_0002416", + "lbl" : "logical macro assertion", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000069", "http://www.ncbi.nlm.nih.gov/pubmed/3065587" ] + "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." }, - "comments" : [ "This phenomenon is usually due to gene conversion process." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "plerologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000069" + "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "in plerology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000066", + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Biological homology that involves parts of the same organism.", - "xrefs" : [ "http://dx.doi.org/10.1146/annurev.es.20.110189.000411", "http://purl.obolibrary.org/obo/HOM_0000066" ] + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "iterative homologous to", - "xrefs" : [ ] + "pred" : "hasRelatedSynonym", + "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000066" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002419", + "lbl" : "annotation property cardinality", "type" : "PROPERTY", - "lbl" : "in iterative homology relationship with" + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000060", + "id" : "http://purl.obolibrary.org/obo/RO_0002420", + "lbl" : "logical macro assertion on a class", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss.", - "xrefs" : [ "http://dx.doi.org/10.1146/annurev.genet.39.073003.114725", "http://purl.obolibrary.org/obo/HOM_0000060", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] + "val" : "A logical macro assertion whose domain is an IRI for a class" }, - "comments" : [ "The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "apparent 1:1 orthology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "apparent orthologous to", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "1:1 paralogy", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "pseudoorthology", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000060" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002421", + "lbl" : "logical macro assertion on a property", "type" : "PROPERTY", - "lbl" : "in apparent orthology relationship with" + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a property" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000061", + "id" : "http://purl.obolibrary.org/obo/RO_0002422", + "lbl" : "logical macro assertion on an object property", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer.", - "xrefs" : [ "http://dx.doi.org/10.1146/annurev.genet.39.073003.114725", "http://purl.obolibrary.org/obo/HOM_0000061" ] - }, - "comments" : [ "These genes may come out as paralogs in a single-genome analysis." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "pseudoparalogous to", - "xrefs" : [ ] - } ], + "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "lbl" : "logical macro assertion on an annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002424", + "lbl" : "differs in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This is an exploratory relation" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000061" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" } ] - }, - "type" : "PROPERTY", - "lbl" : "in pseudoparalogy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004096", + "id" : "http://purl.obolibrary.org/obo/RO_0002425", + "lbl" : "differs in attribute of", + "type" : "PROPERTY", "meta" : { - "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], - "deprecated" : true - }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "lbl" : "differs in attribute", "type" : "PROPERTY", - "lbl" : "DEPRECATED inheres in" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000048", + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Orthology that involves two genes that experienced duplications more recent than the species split that created them.", - "xrefs" : [ "http://dx.doi.org/10.1038/415741a", "http://purl.obolibrary.org/obo/HOM_0000048", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] + "val" : "inverse of causally upstream of or within" }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "co-orthology", - "xrefs" : [ ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "hasRelatedSynonym", - "val" : "trans-homology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "many-to-many orthology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "trans-orthology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "many:many orthology", - "xrefs" : [ ] - }, { - "pred" : "hasExactSynonym", - "val" : "many to many orthologous to", - "xrefs" : [ ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000048" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, - "type" : "PROPERTY", - "lbl" : "in many to many orthology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000049", + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paralogy that involves genes from the same species.", - "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000049", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "within-species paralogous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000049" - }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "in within-species paralogy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004097", - "meta" : { - "deprecated" : true - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", "type" : "PROPERTY", - "lbl" : "DEPRECATED bearer of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000053", "meta" : { "definition" : { - "val" : "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.", - "xrefs" : [ "http://dx.doi.org/10.1007/BF00173425", "http://dx.doi.org/10.1016/S0168-9525(00)02005-9", "http://purl.obolibrary.org/obo/HOM_0000053" ] + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "synologous to", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/HOM_0000053" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/elements/1.1/creator", - "val" : "http://bgee.unil.ch" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] - }, - "type" : "PROPERTY", - "lbl" : "in synology relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000054", + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Orthology that involves functional equivalent genes with retention of the ancestral function.", - 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}, - "type" : "PROPERTY", - "lbl" : "in syngeny relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_HOM0000055", + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "lbl" : "molecularly interacts with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment.", - "xrefs" : [ "http://dx.doi.org/10.1016/S0168-9525(00)02005-9", "http://purl.obolibrary.org/obo/HOM_0000055", "ISBN:978-0878932665" ] + "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "iterative paralogy", - "xrefs" : [ ] + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - 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"val" : "http://purl.obolibrary.org/obo/HOM_0000050" + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" } ] - }, - "type" : "PROPERTY", - "lbl" : "in between-species paralogy relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012002", + "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "lbl" : "preys on", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant", - "xrefs" : [ ] + "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" }, { - 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"lbl" : "indirectly regulates" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012010", "meta" : { - "definition" : { - "val" : "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2022-09-26T06:06:20Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Bees pollinate Flowers" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/pollinates" } ] - }, - "type" : "PROPERTY", - "lbl" : "removes input for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012011", + "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "lbl" : "pollinated by", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.", - "xrefs" : [ ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2022-09-26T06:07:17Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has polinator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasPollinator" } ] - }, - "type" : "PROPERTY", - "lbl" : "indirectly causally upstream of" + } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", + "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "lbl" : "acquires nutrients from", "type" : "PROPERTY", - "lbl" : "has_narrow_synonym" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004050", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-14T00:03:24Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." } ] - }, - "type" : "PROPERTY", - "lbl" : "is negative form of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "id" : "http://purl.obolibrary.org/obo/RO_0002458", + "lbl" : "preyed upon by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.", - "xrefs" : [ ] + "val" : "inverse of preys on" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "triggered by process", - "xrefs" : [ "RO:cjm" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6996-0040" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-8461-9745" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has predator" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of predation interaction with" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + "val" : "http://eol.org/schema/terms/HasPredator" }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" } ] - }, - "type" : "PROPERTY", - "lbl" : "realized in response to" + } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion", + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "lbl" : "is vector for", "type" : "PROPERTY", - "lbl" : "has_obo_format_version" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004047", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:55:19Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally upstream of or within, positive effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "id" : "http://purl.obolibrary.org/obo/RO_0002460", + "lbl" : "has vector", + "type" : "PROPERTY", "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:55:05Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally upstream of or within, negative effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004049", + "id" : "http://purl.obolibrary.org/obo/RO_0002461", + "lbl" : "partner in", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-14T00:03:16Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" } ] - }, - "type" : "PROPERTY", - "lbl" : "is positive form of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004048", + "id" : "http://purl.obolibrary.org/obo/RO_0002462", + "lbl" : "subject participant in", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-03-13T23:59:29Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." } ] - }, - "type" : "PROPERTY", - "lbl" : "is directional form of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", "meta" : { - "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "io" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002464", + "lbl" : "helper property (not for use in curation)", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002465", + "lbl" : "is symbiosis", "type" : "PROPERTY", - "lbl" : "starts during" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "id" : "http://purl.obolibrary.org/obo/RO_0002466", + "lbl" : "is commensalism", + "type" : "PROPERTY", "meta" : { - "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "during" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "d" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002467", + "lbl" : "is mutualism", "type" : "PROPERTY", - "lbl" : "happens during" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "id" : "http://purl.obolibrary.org/obo/RO_0002468", + "lbl" : "is parasitism", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:58:44Z" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", "type" : "PROPERTY", - "lbl" : "disease arises from alteration in structure" + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", "meta" : { - "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "o" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "overlaps" + "val" : "is subject of eating interaction with" } ] - }, - "type" : "PROPERTY", - "lbl" : "ends during" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", "meta" : { - "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends_at_start_of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "meets" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/BFO_0000063" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "eaten by" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" } ] - }, - "type" : "PROPERTY", - "lbl" : "immediately precedes" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004036", + "id" : "http://purl.obolibrary.org/obo/RO_0002472", + "lbl" : "is evidence for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation.", - "xrefs" : [ ] + "val" : "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/creator", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "nominally disjoint with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative", - "xrefs" : [ ] + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:53:22Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002474", + "lbl" : "dispositional interpretation", "type" : "PROPERTY", - "lbl" : "acts upstream of, negative effect" + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "id" : "http://purl.obolibrary.org/obo/RO_0002475", + "lbl" : "has no connections with", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "definition" : { + "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no connection with" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:49:30Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" } ] - }, - "type" : "PROPERTY", - "lbl" : "acts upstream of or within, positive effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.", - "xrefs" : [ ] + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-25T23:20:13Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." } ] - }, - "type" : "PROPERTY", - "lbl" : "enables subfunction" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive", - "xrefs" : [ ] + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:53:14Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "acts upstream of, positive effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-01-26T23:49:51Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "acts upstream of or within, negative effect" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004029", + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.", - "xrefs" : [ ] + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:50:53Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has feature" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016301", - "type" : "CLASS", - "lbl" : "kinase activity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.", - "xrefs" : [ ] + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:45:49Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "realized in response to stimulus" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0014001", + "id" : "http://purl.obolibrary.org/obo/RO_0002481", + "lbl" : "is kinase activity", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0001-5208-3432" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has infectious agent" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "id" : "http://purl.obolibrary.org/obo/RO_0002482", + "lbl" : "is ubiquitination", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Primitive instance level timing relation between events" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "<=" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002483", + "lbl" : "inherited annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002484", + "lbl" : "curator guidance link", "type" : "PROPERTY", - "lbl" : "before or simultaneous with" + "meta" : { + "definition" : { + "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", "meta" : { - "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "simultaneous with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", "meta" : { - "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "before" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004025", + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease causes dysfunction of (disease to anatomical entity)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:58:20Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." } ] - }, - "type" : "PROPERTY", - "lbl" : "disease causes dysfunction of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "during which starts" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004024", + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process.", - "xrefs" : [ ] + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:51:09Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease causes disruption of (disease to process)" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease causes disruption of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "starts before" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004027", + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity", - "xrefs" : [ ] + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "exists during" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-12-26T19:37:31Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has inflammation site" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004026", + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.", - "xrefs" : [ ] + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T04:06:02Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has location" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004021", + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.", - "xrefs" : [ ] + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:37:52Z" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease has basis in disruption of (disease to process)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has basis in disruption of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "during which ends" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", "meta" : { - "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "di" + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" } ] - }, - "type" : "PROPERTY", - "lbl" : "encompasses" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004020", + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.", - "xrefs" : [ ] + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "disease has basis in dysfunction of (disease to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:29:32Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has basis in dysfunction of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004023", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:50:54Z" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", "type" : "PROPERTY", - "lbl" : "causal relationship with disease as subject" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002086", "meta" : { - "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "ends after" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", "meta" : { - "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "David Osumi-Sutherland" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts_at_end_of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, - "type" : "PROPERTY", - "lbl" : "immediately preceded by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004022", + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.", - "xrefs" : [ ] + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:46:07Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has basis in feature" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004018", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:20:29Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] - }, - "type" : "PROPERTY", - "lbl" : "is basis for realizable" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004017", + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:20:01Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] - }, - "type" : "PROPERTY", - "lbl" : "realizable has basis in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004019", + "id" : "http://purl.obolibrary.org/obo/RO_0002503", + "lbl" : "towards", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T03:26:47Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" } ] - }, - "type" : "PROPERTY", - "lbl" : "disease has basis in" - }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", - "type" : "PROPERTY", - "lbl" : "has_broad_synonym" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005634", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/go.owl" - } ] - }, - "type" : "CLASS", - "lbl" : "nucleus" + } }, { - "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002504", + "lbl" : "always present in taxon", "type" : "PROPERTY", - "lbl" : "eco subset" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004014", "meta" : { "definition" : { - "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].", - "xrefs" : [ ] + "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brain always_present_in_taxon 'Vertebrata'" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "forelimb always_present_in_taxon Euarchontoglires" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:57:07Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "never lost in" } ] - }, - "type" : "PROPERTY", - "lbl" : "is causal somatic mutation in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004013", + "id" : "http://purl.obolibrary.org/obo/RO_0002505", + "lbl" : "has intermediate", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].", - "xrefs" : [ ] + "val" : "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:56:40Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has intermediate product" } ] - }, - "type" : "PROPERTY", - "lbl" : "is causal germline mutation in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004016", + "id" : "http://purl.obolibrary.org/obo/RO_0002506", + "lbl" : "causal relation between entities", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:58:43Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317346" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] - }, - "type" : "PROPERTY", - "lbl" : "is causal germline mutation partially giving rise to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004015", + "id" : "http://purl.obolibrary.org/obo/RO_0002507", + "lbl" : "determined by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].", - "xrefs" : [ ] + "val" : "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:57:43Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A coral reef environment is determined by a particular coral reef" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317345" - } ] - }, - "type" : "PROPERTY", - "lbl" : "is causal susceptibility factor for" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004010", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/24330602" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:53:08Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determined by (system to material entity)" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "is genetic basis for condition" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004012", + "id" : "http://purl.obolibrary.org/obo/RO_0002508", + "lbl" : "determines", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].", - 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" + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:45:54Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has material basis in germline mutation in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0004002", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-11-05T02:45:37Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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It is intended as a grouping for a more specific relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "condition has genetic basis in" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016772", - "type" : "CLASS", - "lbl" : "transferase activity, transferring phosphorus-containing groups" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000141", - "type" : "CLASS", - "lbl" : "immaterial entity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b", - "xrefs" : [ ] + "val" : "inverse of has start sequence" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "connected to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002171", + "id" : "http://purl.obolibrary.org/obo/RO_0002518", + "lbl" : "has end sequence", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.", - "xrefs" : [ ] + "val" : "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "non-overlapping with" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "shares no parts with" + "val" : "ended by" }, { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX owl: \nPREFIX part_of: \nPREFIX mutually_spatially_disjoint_with: \nCONSTRUCT {\n part_of: a owl:ObjectProperty .\n [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?x ;\n owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?y\n ]\n ]\n}\nWHERE {\n ?x mutually_spatially_disjoint_with: ?y .\n}" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/RO_0002163" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "mutually spatially disjoint with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015006", - "meta" : { - "definition" : { - "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002519", + "lbl" : "is end sequence of", "type" : "PROPERTY", - "lbl" : "different in magnitude relative to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015007", "meta" : { "definition" : { - "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "inverse of has end sequence" }, - "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] - }, - "type" : "PROPERTY", - "lbl" : "increased in magnitude relative to" + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "id" : "http://purl.obolibrary.org/obo/RO_0002520", + "lbl" : "is consecutive sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." }, - "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] - }, - "type" : "PROPERTY", - "lbl" : "decreased in magnitude relative to" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the SO paper, this was defined as an instance-type relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015009", - "meta" : { - "definition" : { - "val" : "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002521", + "lbl" : "is sequentially aligned with", "type" : "PROPERTY", - "lbl" : "similar in magnitude relative to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002176", "meta" : { "definition" : { - "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.", - "xrefs" : [ ] + "val" : "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The M8 connects Glasgow and Edinburgh" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "connects" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "lbl" : "bounds sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.", - "xrefs" : [ ] + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "attached to part of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "id" : "http://purl.obolibrary.org/obo/RO_0002523", + "lbl" : "is bound by sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.", - "xrefs" : [ ] + "val" : "inverse of bounds sequence of" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "supplies" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "lbl" : "has subsequence", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.", - "xrefs" : [ ] + "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contains" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - } ] - }, - "type" : "PROPERTY", - "lbl" : "drains" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002172", - "meta" : { - "definition" : { - "val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon.", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "taxonomic class assertion" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002173", - "meta" : { - "definition" : { - "val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "lbl" : "is subsequence of", "type" : "PROPERTY", - "lbl" : "ambiguous for taxon" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002174", "meta" : { "definition" : { - "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.", - "xrefs" : [ ] + "val" : "inverse of has subsequence" }, - "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained by" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "dubious for taxon" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "lbl" : "overlaps sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S", - "xrefs" : [ ] + "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." }, - "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - }, { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "present in taxon" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015015", + "id" : "http://purl.obolibrary.org/obo/RO_0002527", + "lbl" : "does not overlap sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", - "xrefs" : [ "PMID:19243617" ] + "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "disconnected from" }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "has high plasma membrane amount" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "lbl" : "is upstream of sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", - "xrefs" : [ "PMID:19243617" ] + "val" : "inverse of downstream of sequence of" }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1940-6740" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "http://orcid.org/0000-0003-1617-8244" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "has low plasma membrane amount" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "lbl" : "is downstream of sequence of", "type" : "PROPERTY", - "lbl" : "has relative magnitude" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015011", "meta" : { "definition" : { - "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." }, - "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] - }, - "type" : "PROPERTY", - "lbl" : "has cross section" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015012", - "meta" : { - "definition" : { - "val" : "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "comments" : [ "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality." ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002530", + "lbl" : "is immediately downstream of sequence of", "type" : "PROPERTY", - "lbl" : "reciprocal of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002160", "meta" : { "definition" : { - "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.", - "xrefs" : [ ] + "val" : "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002529" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "only in taxon" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "id" : "http://purl.obolibrary.org/obo/RO_0002531", + "lbl" : "is immediately upstream of sequence of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.", - "xrefs" : [ ] + "val" : "inverse of immediately downstream of" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - }, { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" + "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" } ] - }, - "type" : "PROPERTY", - "lbl" : "never in taxon" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "id" : "http://purl.obolibrary.org/obo/RO_0002532", + "lbl" : "sequentially ordered entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.", - "xrefs" : [ ] + "val" : "Any entity that is ordered in discrete units along a linear axis." }, - "comments" : [ "Connects a biological entity to its taxon of origin." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9227-417X" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] - }, - "type" : "PROPERTY", - "lbl" : "in taxon" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "id" : "http://purl.obolibrary.org/obo/RO_0002533", + "lbl" : "sequence atomic unit", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common", - "xrefs" : [ ] + "val" : "Any individual unit of a collection of like units arranged in a linear order" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair." } ] - }, - "type" : "PROPERTY", - "lbl" : "spatially disjoint from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "id" : "http://purl.obolibrary.org/obo/RO_0002534", + "lbl" : "sequence bearer", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.", - "xrefs" : [ ] + "val" : "Any entity that can be divided into parts such that each part is an atomical unit of a sequence" }, - "comments" : [ "VBO calls this homologous_to" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence." } ] - }, - "type" : "PROPERTY", - "lbl" : "shares ancestor with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "id" : "http://purl.obolibrary.org/obo/RO_0002535", + "lbl" : "temporal logical macro assertion on a class", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " } ] - }, - "type" : "PROPERTY", - "lbl" : "serially homologous to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003002", + "id" : "http://purl.obolibrary.org/obo/RO_0002536", + "lbl" : "measurement property has unit", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002537", + "lbl" : "has start time value", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "represses expression of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "id" : "http://purl.obolibrary.org/obo/RO_0002538", + "lbl" : "has end time value", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "a produced_by b iff some process that occurs_in b has_output a.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "produced by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "id" : "http://purl.obolibrary.org/obo/RO_0002539", + "lbl" : "start, days post fertilization", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.", - "xrefs" : [ ] + "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "evolutionarily_descended_from" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ancestral_stucture_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "derived by descent from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003003", + "id" : "http://purl.obolibrary.org/obo/RO_0002540", + "lbl" : "end, days post fertilization", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.", - "xrefs" : [ ] + "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "increases expression of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "id" : "http://purl.obolibrary.org/obo/RO_0002541", + "lbl" : "start, years post birth", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of derived by descent from", - "xrefs" : [ ] + "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1." }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "has derived by descendant" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "id" : "http://purl.obolibrary.org/obo/RO_0002542", + "lbl" : "end, years post birth", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "X continuous_with Y if and only if X and Y share a fiat boundary.", - "xrefs" : [ ] + "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "connected to" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "FMA:85972" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "continuous with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "id" : "http://purl.obolibrary.org/obo/RO_0002543", + "lbl" : "start, months post birth", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x", - "xrefs" : [ ] + "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "proper overlaps" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "partially overlaps" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0003000", + "id" : "http://purl.obolibrary.org/obo/RO_0002544", + "lbl" : "end, months post birth", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.", - "xrefs" : [ ] + "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2" }, - "comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "produces" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000141", - "type" : "CLASS", - "lbl" : "structure" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000412", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002545", + "lbl" : "month of gestation", "type" : "PROPERTY", - "lbl" : "imported from" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002380", "meta" : { "definition" : { - "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y", - "xrefs" : [ ] + "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "FMA:85994" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/2212" + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "branching part of" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002546", + "lbl" : "has developmental stage marker", "type" : "PROPERTY", - "lbl" : "term replaced by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002385", "meta" : { "definition" : { - "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y", - 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"xrefs" : [ ] + "val" : "Count of number of days intervening between the start of the stage and the time of coitum." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "has potential to developmentally induce" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "id" : "http://purl.obolibrary.org/obo/RO_0002548", + "lbl" : "end, days post coitum", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y", - "xrefs" : [ ] + "val" : "Count of number of days intervening between the end of the stage and the time of coitum." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "has potential to develop into" + } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0043005", + "id" : "http://purl.obolibrary.org/obo/RO_0002549", + "lbl" : "start, weeks post birth", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/go.owl" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "CLASS", - "lbl" : "neuron projection" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "id" : "http://purl.obolibrary.org/obo/RO_0002550", + "lbl" : "end, weeks post birth", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" } ] - }, - "type" : "PROPERTY", - "lbl" : "has potential to directly develop into" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "id" : "http://purl.obolibrary.org/obo/RO_0002551", + "lbl" : "has skeleton", + "type" : "PROPERTY", "meta" : { "definition" : { - 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}, - "type" : "PROPERTY", - "lbl" : "proper tributary of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "lbl" : "hyperparasitized by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).", - "xrefs" : [ ] + "val" : "inverse of hyperparasite of" }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "has epiparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has hyperparasite" }, { + "pred" : "hasRelatedSynonym", + "val" : "hyperparasitoidized by" + } ], + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has developmental potential involving" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001241", - "type" : "CLASS", - "lbl" : "physical object quality" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "id" : "http://purl.obolibrary.org/obo/RO_0002555", + "lbl" : "allelopath of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y.", - "xrefs" : [ ] - }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "anastomoses with" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Allelopathy" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/allelopathyYes" }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002556", + "lbl" : "pathogen of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002557", + "lbl" : "has pathogen", "type" : "PROPERTY", - "lbl" : "anabranch of" + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "id" : "http://purl.obolibrary.org/obo/RO_0002558", + "lbl" : "has evidence", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x spatially_coextensive_with y if and inly if x and y have the same location", - "xrefs" : [ ] + "val" : "inverse of is evidence for" }, + "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - 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}, - "type" : "CLASS", - "lbl" : "anatomical entity" + } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000003", + "id" : "http://purl.obolibrary.org/obo/RO_0002562", + "lbl" : "is relational form of process class", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/caro.owl" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" } ] - }, - "type" : "CLASS", - "lbl" : "connected anatomical structure" + } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000007", - "type" : "CLASS", - "lbl" : "immaterial anatomical entity" + "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "lbl" : "interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000006", + "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "lbl" : "molecular interaction relation helper property", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/caro.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "CLASS", - "lbl" : "material anatomical entity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002374", + "id" : "http://purl.obolibrary.org/obo/RO_0002565", + "lbl" : "results in movement of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat", - "xrefs" : [ ] + "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" }, - 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"lbl" : "derived from ancestral fusion of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "lbl" : "causally influences", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.", - "xrefs" : [ ] + "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has fasciculating component" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (entity-centric)" } ] - }, - "type" : "PROPERTY", - "lbl" : "has fasciculating neuron projection" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "lbl" : "biomechanically related to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.", - "xrefs" : [ ] + "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/170" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." } ] - }, - "type" : "PROPERTY", - "lbl" : "in branching relationship with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "id" : "http://purl.obolibrary.org/obo/RO_0002568", + "lbl" : "has muscle antagonist", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.", - "xrefs" : [ ] + "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Tributary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains into" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "inferior epigastric vein tributary_of external iliac vein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Deschutes River tributary_of Columbia River" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dbpedia.org/ontology/drainsTo" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "tributary channel of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://en.wikipedia.org/wiki/Tributary" + "val" : "Wikipedia:Antagonist_(muscle)" } ] - }, - "type" : "PROPERTY", - "lbl" : "tributary of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002134", + "id" : "http://purl.obolibrary.org/obo/RO_0002569", + "lbl" : "has branching part", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R.", - "xrefs" : [ ] + "val" : "inverse of branching part of" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that ( some ( that some Y?)))" + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "innervates" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "lbl" : "conduit for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x", - "xrefs" : [ ] + "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." }, - "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "branch of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Distributary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "distributary channel of" + "val" : "UBERON:cjm" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Deschutes River distributary_of Little Lava Lake" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." } ] - }, - "type" : "PROPERTY", - "lbl" : "distributary of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "id" : "http://purl.obolibrary.org/obo/RO_0002571", + "lbl" : "lumen of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a", - "xrefs" : [ ] + "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to (anatomical structure to anatomical structure)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:cjm" } ] - }, - "type" : "PROPERTY", - "lbl" : "attached to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "id" : "http://purl.obolibrary.org/obo/RO_0002572", + "lbl" : "luminal space of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.", - "xrefs" : [ ] + "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dbpedia.org/property/origin" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has muscle origin" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002130", + "id" : "http://purl.obolibrary.org/obo/RO_0002573", + "lbl" : "has modifier", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.", - "xrefs" : [ ] + "val" : "A relation that holds between an attribute or a qualifier and another attribute." }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has synapse in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that some Y?)" + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." } ] - }, - "type" : "PROPERTY", - "lbl" : "has synaptic terminal in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "id" : "http://purl.obolibrary.org/obo/RO_0002574", + "lbl" : "participates in a biotic-biotic interaction with", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" } ] - }, - "type" : "PROPERTY", - "lbl" : "overlaps" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "id" : "http://purl.obolibrary.org/obo/RO_0002575", + "lbl" : "is direct form of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.", - "xrefs" : [ ] + "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dbpedia.org/property/insertion" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://purl.obolibrary.org/obo/RO_0002423", + "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" + }, { + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has muscle insertion" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_00000428", - "type" : "CLASS", - "lbl" : "biome" - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0000011", - "type" : "CLASS", - "lbl" : "connected anatomical system" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016020", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/go.owl" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" } ] - }, - "type" : "CLASS", - "lbl" : "membrane" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002121", + "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "lbl" : "skeleton of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n\t", - "xrefs" : [ ] + "val" : "inverse of has skeleton" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some (\n\t and some (\n\t http://purl.obolibrary.org/obo/GO_0042734 and some (\n\t and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] - }, - "type" : "PROPERTY", - "lbl" : "dendrite synapsed in" + } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045202", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/go.owl" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0002577", + "lbl" : "system", "type" : "CLASS", - "lbl" : "synapse" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002360", "meta" : { + "definition" : { + "val" : "A material entity consisting of multiple components that are causally integrated." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.jbiomedsem.com/content/4/1/43" } ] - }, - "type" : "PROPERTY", - "lbl" : "has dendrite location" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002120", + "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "lbl" : "directly regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n ", - "xrefs" : [ ] + "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." }, - "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that part_of some ( that some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002356", + "id" : "http://purl.obolibrary.org/obo/RO_0002579", + "lbl" : "is indirect form of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. ", - "xrefs" : [ ] + "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002580", + "lbl" : "logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002581", + "lbl" : "is a defining property chain axiom", "type" : "PROPERTY", - "lbl" : "results in specification of" + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002114", + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a motor neuron and a muscle that it synapses to via a type III bouton.", - "xrefs" : [ ] - }, - "comments" : [ "Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] - }, + "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002583", + "lbl" : "existence starts at end of", "type" : "PROPERTY", - "lbl" : "synapsed_via_type_III_bouton_to" + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "id" : "http://purl.obolibrary.org/obo/RO_0002584", + "lbl" : "has part structure that is capable of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location", - "xrefs" : [ ] + "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "located in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "located_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is located in my head" - }, { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this rat is located in this cage" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "located in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "id" : "http://purl.obolibrary.org/obo/RO_0002585", + "lbl" : "results in closure of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002586", + "lbl" : "results in breakdown of", "type" : "PROPERTY", - "lbl" : "capable of positively regulating" + "meta" : { + "definition" : { + "val" : "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002115", + "id" : "http://purl.obolibrary.org/obo/RO_0002587", + "lbl" : "results in synthesis of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002588", + "lbl" : "results in assembly of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002589", + "lbl" : "results in catabolism of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002590", + "lbl" : "results in disassembly of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002591", + "lbl" : "results in remodeling of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002592", + "lbl" : "results in organization of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a muscle and a motor neuron that synapses to it via a type III bouton.\n", - "xrefs" : [ ] + "val" : "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002593", + "lbl" : "existence ends at start of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002594", + "lbl" : "is relational form of a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "lbl" : "causal relation between material entity and a process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." }, - "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed_by_via_type_III_bouton" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "id" : "http://purl.obolibrary.org/obo/RO_0002596", + "lbl" : "capable of regulating", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c.", - "xrefs" : [ ] + "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pyrethroid -> growth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "lbl" : "capable of negatively regulating", "type" : "PROPERTY", - "lbl" : "results in developmental induction of" + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002599", + "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "lbl" : "capable of positively regulating", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.", - "xrefs" : [ ] + "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "treats" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "renin -> arteriolar smooth muscle contraction" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pazopanib -> pathological angiogenesis" } ] - }, - "type" : "PROPERTY", - "lbl" : "capable of inhibiting or preventing pathological process" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000600", + "id" : "http://purl.obolibrary.org/obo/RO_0002599", + "lbl" : "capable of inhibiting or preventing pathological process", "type" : "PROPERTY", - "lbl" : "elucidation" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0019787", - "type" : "CLASS", - "lbl" : "small conjugating protein ligase activity" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0017001", "meta" : { "definition" : { - "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.", - "xrefs" : [ ] + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "utilizes", - "xrefs" : [ ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pazopanib -> pathological angiogenesis" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A diagnostic testing device utilizes a specimen." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-11-08T12:00:00Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." } ] - }, - "type" : "PROPERTY", - "lbl" : "device utilizes material" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002110", + "id" : "http://purl.obolibrary.org/obo/RO_0002600", + "lbl" : "capable of upregulating or causing pathological process", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. ", - "xrefs" : [ ] + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "benzene -> cancer [CHEBI]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapsed in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "causes disease" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, - "type" : "PROPERTY", - "lbl" : "has postsynaptic terminal in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "id" : "http://purl.obolibrary.org/obo/RO_0002601", + "lbl" : "logical macro assertion involving identity", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.", - "xrefs" : [ ] + "val" : "A shortcut relationship that holds between two entities based on their identity criteria" } - }, - "type" : "PROPERTY", - "lbl" : "is autoimmune trigger for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002594", + "id" : "http://purl.obolibrary.org/obo/RO_0002602", + "lbl" : "in approximate one to one relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis.", - "xrefs" : [ ] + "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds." } - }, - "type" : "PROPERTY", - "lbl" : "is relational form of a class" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "id" : "http://purl.obolibrary.org/obo/RO_0002603", + "lbl" : "is approximately equivalent to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has input", - "xrefs" : [ ] + "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" } ] - }, - "type" : "PROPERTY", - "lbl" : "input of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002111", + "id" : "http://purl.obolibrary.org/obo/RO_0002604", + "lbl" : "is opposite of", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has neurotransmitter" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002605", + "lbl" : "is indistinguishable from", "type" : "PROPERTY", - "lbl" : "releases neurotransmitter" + "meta" : { + "definition" : { + "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "id" : "http://purl.obolibrary.org/obo/RO_0002606", + "lbl" : "is substance that treats", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.", - "xrefs" : [ ] + "val" : "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." }, "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" } ] - }, - "type" : "PROPERTY", - "lbl" : "causal relation between material entity and a process" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "id" : "http://purl.obolibrary.org/obo/RO_0002607", + "lbl" : "is marker for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has output", - "xrefs" : [ ] + "val" : "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be ceded to OBI" } ] - }, - "type" : "PROPERTY", - "lbl" : "output of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "id" : "http://purl.obolibrary.org/obo/RO_0002608", + "lbl" : "process has causal agent", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.", - "xrefs" : [ ] + "val" : "Inverse of 'causal agent in process'" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002609", + "lbl" : "obsolete related via dependence to", "type" : "PROPERTY", - "lbl" : "has allergic trigger" + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002112", + "id" : "http://purl.obolibrary.org/obo/RO_0002610", + "lbl" : "correlated with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Is bouton.", - "xrefs" : [ ] + "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." }, - "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-5948-3092" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Groups both positive and negative correlation" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed_by_via_type_Is_bouton" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002596", + "id" : "http://purl.obolibrary.org/obo/RO_0002611", + "lbl" : "evidential logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002612", + "lbl" : "axiom has evidence", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p.", - "xrefs" : [ ] + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pyrethroid -> growth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." } ] - }, - "type" : "PROPERTY", - "lbl" : "capable of regulating" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "id" : "http://purl.obolibrary.org/obo/RO_0002613", + "lbl" : "axiom contradicted by evidence", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002614", + "lbl" : "is evidence with support from", "type" : "PROPERTY", - "lbl" : "formed as result of" + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." + }, + "comments" : [ "In the Gene Ontology association model, this corresponds to the With/From field" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "id" : "http://purl.obolibrary.org/obo/RO_0002615", + "lbl" : "has model", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.", - "xrefs" : [ ] + "val" : "Inverse of is-model-of" } - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002616", + "lbl" : "related via evidence or inference to", "type" : "PROPERTY", - "lbl" : "has autoimmune trigger" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002113", + "id" : "http://purl.obolibrary.org/obo/RO_0002617", + "lbl" : "is representative IRI for equivalence set", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.", - "xrefs" : [ ] + "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that some ( that some Y?)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapses in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002618", + "lbl" : "visits", "type" : "PROPERTY", - "lbl" : "has presynaptic terminal in" + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/74" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "id" : "http://purl.obolibrary.org/obo/RO_0002619", + "lbl" : "visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002622", + "lbl" : "visits flowers of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002623", + "lbl" : "has flowers visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002624", + "lbl" : "lays eggs in", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002625", + "lbl" : "has eggs laid in by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002626", + "lbl" : "kills", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://github.com/jhpoelen/eol-globi-data/issues/143" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002627", + "lbl" : "is killed by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "lbl" : "directly positively regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.", - "xrefs" : [ ] + "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" } ] - }, - "type" : "PROPERTY", - "lbl" : "capable of negatively regulating" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002355", + "id" : "http://purl.obolibrary.org/obo/RO_0002630", + "lbl" : "directly negatively regulates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.", - "xrefs" : [ ] + "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in structural organization of" + } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0045211", + "id" : "http://purl.obolibrary.org/obo/RO_0002632", + "lbl" : "ectoparasite of", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/go.owl" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" } ] - }, - "type" : "CLASS", - "lbl" : "postsynaptic membrane" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002590", - "type" : "PROPERTY", - "lbl" : "results in disassembly of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002591", + "id" : "http://purl.obolibrary.org/obo/RO_0002633", + "lbl" : "has ectoparasite", "type" : "PROPERTY", - "lbl" : "results in remodeling of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002350", "meta" : { "definition" : { - "val" : "is member of is a mereological relation between a item and a collection.", - "xrefs" : [ ] + "val" : "inverse of ectoparasite of" }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002634", + "lbl" : "endoparasite of", + "type" : "PROPERTY", + "meta" : { + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "lives inside of" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is member of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "member part of" + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An organism that is a member of a population of organisms" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" } ] - }, - "type" : "PROPERTY", - "lbl" : "member of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002592", + "id" : "http://purl.obolibrary.org/obo/RO_0002635", + "lbl" : "has endoparasite", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002636", + "lbl" : "mesoparasite of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c", - "xrefs" : [ ] + "val" : "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" } - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002637", + "lbl" : "has mesoparasite", "type" : "PROPERTY", - "lbl" : "results in organization of" + "meta" : { + "definition" : { + "val" : "inverse of mesoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "id" : "http://purl.obolibrary.org/obo/RO_0002638", + "lbl" : "intercellular endoparasite of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.", - "xrefs" : [ ] + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002639", + "lbl" : "has intercellular endoparasite", "type" : "PROPERTY", - "lbl" : "is allergic trigger for" + "meta" : { + "definition" : { + "val" : "inverse of intercellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "id" : "http://purl.obolibrary.org/obo/RO_0002640", + "lbl" : "intracellular endoparasite of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "has member is a mereological relation between a collection and an item.", - "xrefs" : [ ] + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits host cells." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" } ] - }, - "type" : "PROPERTY", - "lbl" : "has member" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002593", + "id" : "http://purl.obolibrary.org/obo/RO_0002641", + "lbl" : "has intracellular endoparasite", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y).", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "existence ends at start of" + "val" : "inverse of intracellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002349", + "id" : "http://purl.obolibrary.org/obo/RO_0002801", + "lbl" : "co-roosts with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.", - "xrefs" : [ ] + "val" : "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Communal_roosting" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in determination of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002107", + "id" : "http://purl.obolibrary.org/obo/RO_0003000", + "lbl" : "produces", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between a motor neuron and a muscle that it synapses to via a type II bouton.", - "xrefs" : [ ] + "val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." }, - "comments" : [ "Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-5948-3092" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed_via_type_II_bouton_to" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001018", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contained_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "contained in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" - } ] - }, - "type" : "PROPERTY", - "lbl" : "contained in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001019", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "contains" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] - }, - "type" : "PROPERTY", - "lbl" : "contains" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002108", - "meta" : { - "definition" : { - "val" : "Relation between a muscle and a motor neuron that synapses to it via a type II bouton.", - "xrefs" : [ ] - }, - "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-5948-3092" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "lbl" : "produced by", "type" : "PROPERTY", - "lbl" : "synapsed_by_via_type_II_bouton" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002109", "meta" : { "definition" : { - "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton.", - "xrefs" : [ ] + "val" : "a produced_by b iff some process that occurs_in b has_output a." }, - "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-5948-3092" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" + "val" : "https://orcid.org/0000-0001-9114-8737" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed_by_via_type_Ib_bouton" + } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "id" : "http://purl.obolibrary.org/obo/RO_0003002", + "lbl" : "represses expression of", "type" : "PROPERTY", - "lbl" : "shorthand" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002103", "meta" : { "definition" : { - "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. ", - "xrefs" : [ ] + "val" : "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0003-4639-4431" } ] - }, - "type" : "PROPERTY", - "lbl" : "synapsed by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002345", + "id" : "http://purl.obolibrary.org/obo/RO_0003003", + "lbl" : "increases expression of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.", - "xrefs" : [ ] + "val" : "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. 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It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:26:47Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "genomically related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "id" : "http://purl.obolibrary.org/obo/RO_0004020", + "lbl" : "disease has basis in dysfunction of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", - "xrefs" : [ ] + "val" : "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this nucleus derives from this parent nucleus (nuclear division)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this cell derives from this parent cell (cell division)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in dysfunction of (disease to anatomical structure)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "derives_from" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:29:32Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "derives from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "id" : "http://purl.obolibrary.org/obo/RO_0004021", + "lbl" : "disease has basis in disruption of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c involved_in p if and only if c enables some process p', and p' is part of p", - "xrefs" : [ ] + "val" : "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enables part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "actively involved in" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in disruption of (disease to process)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Involved_in" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:37:52Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "involved in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002573", + "id" : "http://purl.obolibrary.org/obo/RO_0004022", + "lbl" : "disease has basis in feature", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between an attribute or a qualifier and another attribute.", - "xrefs" : [ ] + "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:46:07Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has modifier" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002574", + "id" : "http://purl.obolibrary.org/obo/RO_0004023", + "lbl" : "causal relationship with disease as subject", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:50:54Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "participates in a biotic-biotic interaction with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "id" : "http://purl.obolibrary.org/obo/RO_0004024", + "lbl" : "disease causes disruption of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity", - "xrefs" : [ ] + "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this parent cell derives into this cell (cell division)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this parent nucleus derives into this nucleus (nuclear division)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes disruption of (disease to process)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "derives_into" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:51:09Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "derives into" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "id" : "http://purl.obolibrary.org/obo/RO_0004025", + "lbl" : "disease causes dysfunction of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" + "val" : "disease causes dysfunction of (disease to anatomical entity)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:58:20Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "regulates levels of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002333", - "meta" : { - "definition" : { - "val" : "inverse of enables", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0004026", + "lbl" : "disease has location", "type" : "PROPERTY", - "lbl" : "enabled by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002575", "meta" : { "definition" : { - "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y", - "xrefs" : [ ] + "val" : "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" + "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002423", - "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." }, { - "pred" : "http://purl.org/dc/terms/creator", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T04:06:02Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "is direct form of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0040042", + "id" : "http://purl.obolibrary.org/obo/RO_0004027", + "lbl" : "disease has inflammation site", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.", - "xrefs" : [ ] + "val" : "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" }, - "comments" : [ "R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-10-21T19:46:34Z" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/164" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "part-of is homeomorphic for independent continuants." + "val" : "2017-12-26T19:37:31Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "is homeomorphic for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.", - "xrefs" : [ ] + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "UBERON:cjm" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "conduit for" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002571", - "meta" : { - "definition" : { - "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0004029", + "lbl" : "disease has feature", "type" : "PROPERTY", - "lbl" : "lumen of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002569", "meta" : { "definition" : { - "val" : "inverse of branching part of", - "xrefs" : [ ] + "val" : "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:50:53Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has branching part" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "lbl" : "disease arises from alteration in structure", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "c enables p iff c is capable of p and c acts to execute p.", - "xrefs" : [ ] + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "catalyzes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is catalyzing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is executing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "enables" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "lbl" : "enables subfunction", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.", - "xrefs" : [ ] + "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-25T23:20:13Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "functionally related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "lbl" : "acts upstream of or within, positive effect", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p.", - "xrefs" : [ ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "false" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "part of structure that is capable of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002323", - "meta" : { - "definition" : { - "val" : "A mereological relationship or a topological relationship", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:30Z" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" } ] - }, - "type" : "PROPERTY", - "lbl" : "mereotopologically related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002565", + "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "lbl" : "acts upstream of or within, negative effect", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:51Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "results in movement of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "lbl" : "acts upstream of, positive effect", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).", - "xrefs" : [ ] + "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:14Z" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally influences" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "lbl" : "acts upstream of, negative effect", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)", - "xrefs" : [ ] + "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" } ] - }, - "type" : "PROPERTY", - "lbl" : "developmentally related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "id" : "http://purl.obolibrary.org/obo/RO_0004036", + "lbl" : "nominally disjoint with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between elements of a musculoskeletal system or its analogs.", - "xrefs" : [ ] + "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "https://orcid.org/0000-0002-6601-2165" } ] - }, - "type" : "PROPERTY", - "lbl" : "biomechanically related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "colocalizes with" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", + "type" : "PROPERTY", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "contributes to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002568", + "id" : "http://purl.obolibrary.org/obo/RO_0004048", + "lbl" : "is directional form of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.", - "xrefs" : [ ] + "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Antagonist_(muscle)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:59:29Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has muscle antagonist" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000232", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0004049", + "lbl" : "is positive form of", "type" : "PROPERTY", - "lbl" : "curator note" - }, { - "id" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "is defined by" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:16Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0002000", - "meta" : { - "definition" : { - "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", "type" : "PROPERTY", - "lbl" : "defined by construct" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0040035", "meta" : { - "definition" : { - "val" : "This relation groups relations between diseases and any other kind of entity.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-09-26T00:00:32Z" + "val" : "2018-03-14T00:03:24Z" } ] - }, + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004096", + "lbl" : "DEPRECATED inheres in", "type" : "PROPERTY", - "lbl" : "disease relationship" + "meta" : { + "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], + "deprecated" : true + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002561", + "id" : "http://purl.obolibrary.org/obo/RO_0004097", + "lbl" : "DEPRECATED bearer of", + "type" : "PROPERTY", + "meta" : { + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007000", + "lbl" : "has driver", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p", - "xrefs" : [ ] + "val" : "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." }, "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + "val" : "https://github.com/oborel/obo-relations/issues/506" } ] - }, - "type" : "PROPERTY", - "lbl" : "is symmetric relational form of process class" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "id" : "http://purl.obolibrary.org/obo/RO_0007001", + "lbl" : "has disease driver", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship that holds via some environmental process", - "xrefs" : [ ] + "val" : "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" } ] - }, - "type" : "PROPERTY", - "lbl" : "evolutionarily related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002562", + "id" : "http://purl.obolibrary.org/obo/RO_0008501", + "lbl" : "epiphyte of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process", - "xrefs" : [ ] + "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Epiphyte" } ] - }, - "type" : "PROPERTY", - "lbl" : "is relational form of process class" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0040036", + "id" : "http://purl.obolibrary.org/obo/RO_0008502", + "lbl" : "has epiphyte", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p has anatomical participant c iff p has participant c, and c is an anatomical entity", - "xrefs" : [ ] + "val" : "inverse of epiphyte of" }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2018-09-26T01:08:58Z" - } ] - }, - "type" : "PROPERTY", - "lbl" : "results in changes to anatomical or cellular structure" + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002563", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0008503", + "lbl" : "kleptoparasite of", "type" : "PROPERTY", - "lbl" : "interaction relation helper property" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002321", "meta" : { "definition" : { - "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)", - "xrefs" : [ ] + "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" } ] - }, - "type" : "PROPERTY", - "lbl" : "ecologically related to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002322", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "adapted for" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0008504", + "lbl" : "kleptoparasitized by", "type" : "PROPERTY", - "lbl" : "confers advantage in" + "meta" : { + "definition" : { + "val" : "inverse of kleptoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "id" : "http://purl.obolibrary.org/obo/RO_0008505", + "lbl" : "creates habitat for", + "type" : "PROPERTY", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "definition" : { + "val" : "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008506", + "lbl" : "ecologically co-occurs with", "type" : "PROPERTY", - "lbl" : "molecular interaction relation helper property" + "meta" : { + "definition" : { + "val" : "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002560", + "id" : "http://purl.obolibrary.org/obo/RO_0008507", + "lbl" : "lays eggs on", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - } ] - }, + "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008508", + "lbl" : "has eggs laid on by", "type" : "PROPERTY", - "lbl" : "is asymmetric relational form of process class" + "meta" : { + "definition" : { + "val" : "inverse of lays eggs on" + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002558", + "id" : "http://purl.obolibrary.org/obo/RO_0009001", + "lbl" : "has substance added", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of is evidence for", - "xrefs" : [ ] + "val" : "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." }, - "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/25052702" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "muffin 'has substance added' some 'baking soda'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0002-8844-9165" } ] - }, - "type" : "PROPERTY", - "lbl" : "has evidence" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "id" : "http://purl.obolibrary.org/obo/RO_0009002", + "lbl" : "has substance removed", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'egg white' 'has substance removed' some 'egg yolk'" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influenced by (entity-centric)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" } ] - }, - "type" : "PROPERTY", - "lbl" : "causally influenced by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "id" : "http://purl.obolibrary.org/obo/RO_0009003", + "lbl" : "immersed in", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of hyperparasite of", - "xrefs" : [ ] + "val" : "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "has epiparasite", - "xrefs" : [ ] + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardines 'immersed in' some 'oil and mustard'" }, { - "pred" : "hasRelatedSynonym", - "val" : "has hyperparasite", - "xrefs" : [ ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { - "pred" : "hasRelatedSynonym", - "val" : "hyperparasitoidized by", - "xrefs" : [ ] - } ], - "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0002-8844-9165" } ] - }, - "type" : "PROPERTY", - "lbl" : "hyperparasitized by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002312", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0009004", + "lbl" : "has consumer", "type" : "PROPERTY", - "lbl" : "evolutionary variant of" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002555", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "definition" : { + "val" : "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Allelopathy" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardine has consumer some homo sapiens" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://eol.org/schema/terms/allelopathyYes" + "val" : "https://orcid.org/0000-0002-8844-9165" } ] - }, - "type" : "PROPERTY", - "lbl" : "allelopath of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "id" : "http://purl.obolibrary.org/obo/RO_0009005", + "lbl" : "has primary substance added", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.", - "xrefs" : [ ] + "val" : "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bread 'has primary substance added' some 'flour'" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "regulates localization of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" } ] - }, - "type" : "PROPERTY", - "lbl" : "transports or maintains localization of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "lbl" : "realized in response to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.", - "xrefs" : [ ] + "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "triggered by process", + "xrefs" : [ "RO:cjm" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" } ] - }, - "type" : "PROPERTY", - "lbl" : "characteristic of part of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002556", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0010001", + "lbl" : "generically depends on", "type" : "PROPERTY", - 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"val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x", - "xrefs" : [ ] + "val" : "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "contains" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" } ] - }, - "type" : "PROPERTY", - "lbl" : "has subsequence" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "id" : "http://purl.obolibrary.org/obo/RO_0015001", + "lbl" : "has exemplar data", + "type" : "PROPERTY", "meta" : { "definition" : { - 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}, - "type" : "PROPERTY", - "lbl" : "is downstream of sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002520", + "id" : "http://purl.obolibrary.org/obo/RO_0015002", + "lbl" : "exemplar data of", + "type" : "PROPERTY", "meta" : { - "definition" : { - "val" : "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y.", - "xrefs" : [ ] - }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "In the SO paper, this was defined as an instance-type relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + "val" : "https://orcid.org/0000-0002-5260-9315" } ] - }, - "type" : "PROPERTY", - "lbl" : "is consecutive sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002514", + "id" : "http://purl.obolibrary.org/obo/RO_0015003", + "lbl" : "subcluster of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. 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In these cases it is recommended to make a more specific cell class restricted to the relevant context." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" - } ] - }, + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015006", + "lbl" : "different in magnitude relative to", "type" : "PROPERTY", - "lbl" : "sequentially adjacent to" + "meta" : { + "definition" : { + "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002516", + "id" : "http://purl.obolibrary.org/obo/RO_0015007", + "lbl" : "increased in magnitude relative to", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence", - "xrefs" : [ ] + "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every CDS has as a start sequence the start codon for that transcript" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "lbl" : "decreased in magnitude relative to", "type" : "PROPERTY", - "lbl" : "has start sequence" + "meta" : { + "definition" : { + "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "id" : "http://purl.obolibrary.org/obo/RO_0015009", + "lbl" : "similar in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "lbl" : "has relative magnitude", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015011", + "lbl" : "has cross section", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has start sequence", - "xrefs" : [ ] + "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts" - } ] - }, + "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015012", + "lbl" : "reciprocal of", "type" : "PROPERTY", - "lbl" : "is start sequence of" + "meta" : { + "definition" : { + "val" : "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality." ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002510", + "id" : "http://purl.obolibrary.org/obo/RO_0015015", + "lbl" : "has high plasma membrane amount", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is transcribed from y if and only if x is synthesized from template y", - "xrefs" : [ ] + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" } ] - }, - "type" : "PROPERTY", - "lbl" : "transcribed from" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002511", + "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "lbl" : "has low plasma membrane amount", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of transcribed from", - "xrefs" : [ ] + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" } ] - }, - "type" : "PROPERTY", - "lbl" : "transcribed to" + } }, { - "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "id" : "http://purl.obolibrary.org/obo/RO_0016001", + "lbl" : "has phenotype or disease", + "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-09-22T11:05:29Z" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:14Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/subsets/" + "val" : "https://github.com/oborel/obo-relations/issues/478" } ] - }, - "type" : "PROPERTY", - "lbl" : "valid_for_go_annotation_extension" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002512", + "id" : "http://purl.obolibrary.org/obo/RO_0016002", + "lbl" : "has disease", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y", - "xrefs" : [ ] + "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:44Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" } ] - }, - "type" : "PROPERTY", - "lbl" : "ribosomal translation of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002513", + "id" : "http://purl.obolibrary.org/obo/RO_0016004", + "lbl" : "has exposure medium", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of ribosomal translation of", - "xrefs" : [ ] + "val" : "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + "val" : "ExO:0000083" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-12-14T20:41:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7463-6306" } ] - }, - "type" : "PROPERTY", - "lbl" : "ribosomally translates to" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002518", + "id" : "http://purl.obolibrary.org/obo/RO_0017001", + "lbl" : "device utilizes material", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence", - "xrefs" : [ ] + "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "utilizes" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" + "val" : "A diagnostic testing device utilizes a specimen." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ended by" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "https://orcid.org/0000-0003-2620-0345" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-11-08T12:00:00Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has end sequence" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002519", + "id" : "http://purl.obolibrary.org/obo/RO_0018001", + "lbl" : "is myristoyltransferase activity", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of has end sequence", - "xrefs" : [ ] + "val" : "Helper relation for OWL definition of RO:0018002 myristoylates" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] - }, - "type" : "PROPERTY", - "lbl" : "is end sequence of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002503", + "id" : "http://purl.obolibrary.org/obo/RO_0018002", + "lbl" : "myristoylates", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2", - "xrefs" : [ ] + "val" : "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + "pred" : "http://purl.org/dc/terms/conformsTo", + "val" : "http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] - }, - "type" : "PROPERTY", - "lbl" : "towards" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002504", + "id" : "http://purl.obolibrary.org/obo/RO_0018003", + "lbl" : "myristoylated by", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S", - "xrefs" : [ ] + "val" : "inverse of myristoylates" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "never lost in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "forelimb always_present_in_taxon Euarchontoglires" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "brain always_present_in_taxon 'Vertebrata'" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] - }, - "type" : "PROPERTY", - "lbl" : "always present in taxon" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002505", + "id" : "http://purl.obolibrary.org/obo/RO_0018027", + "lbl" : "is agonist of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c", - "xrefs" : [ ] + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" + "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has intermediate product" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "has intermediate" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002506", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P3772" } ] - }, - "type" : "PROPERTY", - "lbl" : "causal relation between entities" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002500", - "meta" : { - "definition" : { - "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process", - "xrefs" : [ ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_0018028", + "lbl" : "is inverse agonist of", "type" : "PROPERTY", - "lbl" : "causal agent in process" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002501", "meta" : { "definition" : { - "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.", - "xrefs" : [ ] + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223)" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "causal relation between processes" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002502", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/BFO_0000169" + "val" : "https://www.wikidata.org/wiki/Property:P9275" } ] - }, - "type" : "PROPERTY", - "lbl" : "depends on" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002507", + "id" : "http://purl.obolibrary.org/obo/RO_0018029", + "lbl" : "is antagonist of", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.", - "xrefs" : [ ] + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "determined by (system to material entity)" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-4366-3088" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/24330602" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A coral reef environment is determined by a particular coral reef" + "val" : "tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753)" }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P3773" } ] - }, - "type" : "PROPERTY", - "lbl" : "determined by" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002508", + "id" : "http://purl.obolibrary.org/obo/RO_0019000", + "lbl" : "regulates characteristic", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of determined by", - "xrefs" : [ ] + "val" : "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "determines (material entity to system)" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] - }, - "type" : "PROPERTY", - "lbl" : "determines" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002509", + "id" : "http://purl.obolibrary.org/obo/RO_0019001", + "lbl" : "positively regulates characteristic", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.", - "xrefs" : [ ] + "val" : "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - }, - "type" : "PROPERTY", - "lbl" : "determined by part of" - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0010000", - "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/caro.owl" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] - }, - "type" : "CLASS", - "lbl" : "multicellular anatomical structure" + } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "id" : "http://purl.obolibrary.org/obo/RO_0019002", + "lbl" : "negatively regulates characteristic", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] - }, - "lbl" : "obsolescence reason specification" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009002", + "id" : "http://purl.obolibrary.org/obo/RO_0019501", + "lbl" : "confers susceptibility to condition", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time.", - "xrefs" : [ ] + "val" : "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'egg white' 'has substance removed' some 'egg yolk'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-8844-9165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-4142-7153" } ] - }, - "type" : "PROPERTY", - "lbl" : "has substance removed" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009001", + "id" : "http://purl.obolibrary.org/obo/RO_0040035", + "lbl" : "disease relationship", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time.", - "xrefs" : [ ] + "val" : "This relation groups relations between diseases and any other kind of entity." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-8844-9165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "muffin 'has substance added' some 'baking soda'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T00:00:32Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has substance added" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009005", + "id" : "http://purl.obolibrary.org/obo/RO_0040036", + "lbl" : "results in changes to anatomical or cellular structure", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance.", - "xrefs" : [ ] + "val" : "p has anatomical participant c iff p has participant c, and c is an anatomical entity" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-8844-9165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bread 'has primary substance added' some 'flour'" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T01:08:58Z" } ] - }, - "type" : "PROPERTY", - "lbl" : "has primary substance added" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009004", + "id" : "http://purl.obolibrary.org/obo/RO_0040042", + "lbl" : "is homeomorphic for", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect.", - "xrefs" : [ ] + "val" : "R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C." }, + "comments" : [ "R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "sardine has consumer some homo sapiens" + "val" : "part-of is homeomorphic for independent continuants." }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-8844-9165" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-10-21T19:46:34Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/164" } ] - }, - "type" : "PROPERTY", - "lbl" : "has consumer" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0009003", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "lbl" : "in similarity relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance.", - "xrefs" : [ ] + "val" : "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000000", "BGEE:curator" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "sameness" + }, { + "pred" : "hasExactSynonym", + "val" : "similar to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "correspondence", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "resemblance" + } ], + "xrefs" : [ { + "val" : "ECO:0000041" + }, { + "val" : "SO:similar_to" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "sardines 'immersed in' some 'oil and mustard'" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add homeomorphy axiom" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-8844-9165" + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000000" } ] - }, - "type" : "PROPERTY", - "lbl" : "immersed in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002602", - "meta" : { - "definition" : { - "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds.", - "xrefs" : [ ] - } - }, + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000001", + "lbl" : "in homology relationship with", "type" : "PROPERTY", - "lbl" : "in approximate one to one relationship with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002603", "meta" : { "definition" : { - "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y", - "xrefs" : [ ] + "val" : "Similarity that results from common evolutionary origin.", + "xrefs" : [ "http://dx.doi.org/10.1002/bies.950180611", "http://dx.doi.org/10.1002/jmor.1051730307", "http://dx.doi.org/10.1007/BF02814480", "http://purl.obolibrary.org/obo/HOM_0000001" ] }, + "comments" : [ "This broad definition encompasses all the working definitions proposed so far in the literature." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homologous to" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. 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"pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000022" } ] - }, - "type" : "PROPERTY", - "lbl" : "directly regulates quantity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0007000", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000023", + "lbl" : "in in-paralogy relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity.", - "xrefs" : [ ] + "val" : "Paralogy that results from a lineage-specific duplication subsequent to a given speciation event.", + "xrefs" : [ "http://dx.doi.org/10.1146/annurev.genet.39.073003.114725", "http://purl.obolibrary.org/obo/HOM_0000023" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in-paralogous to" + }, { + "pred" : "hasExactSynonym", + "val" : "inparalogy" + }, { + "pred" : "hasExactSynonym", + "val" : "symparalogy" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/506" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-8910-9851" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000023" } ] - }, - "type" : "PROPERTY", - "lbl" : "has driver" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0011024", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000024", + "lbl" : "in out-paralogy relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B.", - "xrefs" : [ ] + "val" : "Paralogy that results from a duplication preceding a given speciation event.", + "xrefs" : [ "http://dx.doi.org/10.1146/annurev.genet.39.073003.114725", "http://purl.obolibrary.org/obo/HOM_0000024" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "alloparalogy" + }, { + "pred" : "hasExactSynonym", + "val" : "out-paralogous to" + }, { + "pred" : "hasExactSynonym", + "val" : "outparalogy" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000024" } ] - }, - "type" : "PROPERTY", - "lbl" : "indirectly positively regulates quantity of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0007001", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000025", + "lbl" : "in pro-orthology relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes.", - "xrefs" : [ ] + "val" : "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A.", + "xrefs" : [ "http://dx.doi.org/10.1006/scdb.1999.0338", "http://dx.doi.org/10.1038/nrg2099", "http://purl.obolibrary.org/obo/HOM_0000025" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "pro-orthologous to" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-8910-9851" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/oborel/obo-relations/issues/506" + "val" : "http://purl.obolibrary.org/obo/HOM_0000025" } ] - }, - "type" : "PROPERTY", - "lbl" : "has disease driver" - }, { - "id" : "http://purl.obolibrary.org/obo/CARO_0030000", - "type" : "CLASS", - "lbl" : "biological entity" + } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0042995", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000026", + "lbl" : "in semi-orthology relationship with", + "type" : "PROPERTY", "meta" : { + "definition" : { + "val" : "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B.", + "xrefs" : [ "http://dx.doi.org/10.1006/scdb.1999.0338", "http://dx.doi.org/10.1038/nrg2099", "http://purl.obolibrary.org/obo/HOM_0000026" ] + }, + "comments" : [ "The converse of pro-orthologous." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "semi-orthologous to" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/go.owl" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000026" } ] - }, - "type" : "CLASS", - "lbl" : "cell projection" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000027", + "lbl" : "in serial homology relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a core relation that holds between a part and its whole", - "xrefs" : [ ] + "val" : "Iterative homology that involves structures arranged along the main body axis.", + "xrefs" : [ "http://dx.doi.org/10.1146/annurev.es.20.110189.000411", "http://purl.obolibrary.org/obo/HOM_0000027" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "serial homologous to" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + "pred" : "hasRelatedSynonym", + "val" : "homonomy" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + "val" : "http://purl.obolibrary.org/obo/HOM_0000027" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000028", + "lbl" : "in heterochronous homology relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000028", "ISBN:978-0674639416" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "heterochronous homologous to" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is part of my body (continuant parthood, two material entities)" + "pred" : "hasExactSynonym", + "val" : "heterochrony" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + "val" : "http://purl.obolibrary.org/obo/HOM_0000028" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000029", + "lbl" : "in paedomorphorsis relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles.", + "xrefs" : [ "http://en.wikipedia.org/wiki/Pedomorphosis", "http://purl.obolibrary.org/obo/HOM_0000029", "ISBN:978-0674639416" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "juvenification" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is part of" + "pred" : "hasExactSynonym", + "val" : "pedomorphosis" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this day is part of this year (occurrent parthood)" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000031" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "val" : "http://purl.obolibrary.org/obo/HOM_0000029" } ] - }, - "type" : "PROPERTY", - "lbl" : "part of" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000055", - "meta" : { - "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this disease course realizes this disease" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this investigation realizes this investigator role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "realizes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this shattering realizes this fragility" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/iao.owl" - } ] - }, - "type" : "PROPERTY", - "lbl" : "realizes" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000030", + "lbl" : "in peramorphosis relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "a core relation that holds between a whole and its part", - "xrefs" : [ ] + "val" : "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits.", + "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000030" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this year has part this day (occurrent parthood)" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has part my brain (continuant parthood, two material entities)" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000030" } ] - }, - "type" : "PROPERTY", - "lbl" : "has part" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000054", - "meta" : { - "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "realized_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this disease is realized in this disease course" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this fragility is realized in this shattering" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is realized by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this investigator role is realized in this investigation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" - } ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000031", + "lbl" : "in progenesis relationship with", "type" : "PROPERTY", - "lbl" : "realized in" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001900", "meta" : { "definition" : { - "val" : "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.", - "xrefs" : [ ] + "val" : "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage.", + "xrefs" : [ "http://en.wikipedia.org/wiki/Progenesis", "http://purl.obolibrary.org/obo/HOM_0000031", "ISBN:978-0674639416" ] }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://oborel.github.io/obo-relations/temporal-semantics/" + "val" : "http://purl.obolibrary.org/obo/HOM_0000031" } ] - }, - "type" : "PROPERTY", - "lbl" : "temporal interpretation" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001901", - "meta" : { - "definition" : { - "val" : "\n\n## Elucidation\n\nThis is used when the statement/axiom is assumed to hold true 'eternally'\n\n## How to interpret (informal)\n\nFirst the \"atemporal\" FOL is derived from the OWL using the standard\ninterpretation. This axiom is temporalized by embedding the axiom\nwithin a for-all-times quantified sentence. The t argument is added to\nall instantiation predicates and predicates that use this relation.\n\n## Example\n\n Class: nucleus\n SubClassOf: part_of some cell\n\n forall t :\n forall n :\n instance_of(n,Nucleus,t)\n implies\n exists c :\n instance_of(c,Cell,t)\n part_of(n,c,t)\n\n## Notes\n\nThis interpretation is *not* the same as an at-all-times relation\n\n", - "xrefs" : [ ] - } - }, - "type" : "INDIVIDUAL", - "lbl" : "axiom holds for all times" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000040", - "meta" : { - "definition" : { - "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "material entity" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013003", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000032", + "lbl" : "in neoteny relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region.", - "xrefs" : [ ] + "val" : "Paedomorphosis that is produced by a retardation of somatic development.", + "xrefs" : [ "http://en.wikipedia.org/wiki/Neoteny", "http://purl.obolibrary.org/obo/HOM_0000032", "ISBN:978-0674639416" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "juvenilization" + }, { + "pred" : "hasExactSynonym", + "val" : "neotenous to" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:45:06Z" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000032" } ] - }, - "type" : "PROPERTY", - "lbl" : "sends synaptic output to region" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001902", - "meta" : { - "definition" : { - "val" : "\n\n## Elucidation\n\nThis is used when the first-order logic form of the relation is\nbinary, and takes no temporal argument.\n\n## Example:\n\n Class: limb\n SubClassOf: develops_from some lateral-plate-mesoderm\n\n forall t, t2:\n forall x :\n instance_of(x,Limb,t)\n implies\n exists y :\n instance_of(y,LPM,t2)\n develops_from(x,y)\n\n\n", - "xrefs" : [ ] - } - }, - "type" : "INDIVIDUAL", - "lbl" : "relation has no temporal argument" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013002", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000033", + "lbl" : "in mimicry relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region.", - "xrefs" : [ ] + "val" : "Convergence that results from co-evolution usually involving an evolutionary arms race.", + "xrefs" : [ "http://en.wikipedia.org/wiki/Mimicry", "http://purl.obolibrary.org/obo/HOM_0000033" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "mimicrous to" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:42:23Z" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000033" } ] - }, - "type" : "PROPERTY", - "lbl" : "receives synaptic input in region" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013001", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000034", + "lbl" : "in 1 to many orthology relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region.", - "xrefs" : [ ] + "val" : "Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other.", + "xrefs" : [ "http://dx.doi.org/10.1038/415741a", "http://purl.obolibrary.org/obo/HOM_0000034", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "has synaptic input or output in", - "xrefs" : [ ] + "val" : "1 to many orthologous to" + }, { + "pred" : "hasExactSynonym", + "val" : "1:many orthology" + }, { + "pred" : "hasExactSynonym", + "val" : "one-to-many orthology" + }, { + "pred" : "hasRelatedSynonym", + "val" : "co-orthology" + }, { + "pred" : "hasRelatedSynonym", + "val" : "many to 1 orthology" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:26:52Z" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000034" } ] - }, - "type" : "PROPERTY", - "lbl" : "has synaptic IO in region" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013007", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000036", + "lbl" : "in many to many homology relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite.", - "xrefs" : [ ] + "val" : "Historical homology that involves two members of a larger set of homologs.", + "xrefs" : [ "http://dx.doi.org/10.1093/molbev/msp002", "http://purl.obolibrary.org/obo/HOM_0000036" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "has sensory terminal in", - "xrefs" : [ ] + "val" : "many to many homologous to" }, { "pred" : "hasExactSynonym", - "val" : "has sensory dendrite location", - "xrefs" : [ ] + "val" : "many-to-many homology" }, { "pred" : "hasExactSynonym", - "val" : "has sensory terminal location", - "xrefs" : [ ] + "val" : "many:many homology " } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-20T12:10:09Z" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000036" } ] - }, - "type" : "PROPERTY", - "lbl" : "has sensory dendrite in" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013006", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000037", + "lbl" : "in 1 to many homology relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion).", - "xrefs" : [ ] + "val" : "Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000037", "BGEE:curator" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "1 to many homologous to" + }, { + "pred" : "hasExactSynonym", + "val" : "one-to-many homology" + }, { + "pred" : "hasRelatedSynonym", + "val" : "1:many homology" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:57:27Z" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000037" } ] - }, - "type" : "PROPERTY", - "lbl" : "sends synaptic output throughout" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013005", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000042", + "lbl" : "in apomorphy relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion).", - "xrefs" : [ ] + "val" : "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000042", "ISBN:978-0252068140" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "apomorphous to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "synapomorphy" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:55:36Z" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000042" } ] - }, - "type" : "PROPERTY", - "lbl" : "receives synaptic input throughout" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013004", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000043", + "lbl" : "in plesiomorphy relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion).", - "xrefs" : [ ] - }, + "val" : "Historical homology that is based on distant shared ancestry.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000043", "ISBN:978-0252068140" ] + }, + "comments" : [ "This term is usually contrasted to apomorphy." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "plesiomorphous to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "symplesiomorphy" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:52:19Z" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000043" } ] - }, - "type" : "PROPERTY", - "lbl" : "has synaptic IO throughout" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013009", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000044", + "lbl" : "in deep homology relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to.", - "xrefs" : [ ] + "val" : "Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution.", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814485", "http://dx.doi.org/10.1038/nature07891", "http://purl.obolibrary.org/obo/HOM_0000044" ] }, - "comments" : [ "Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron." ], + "comments" : [ "Used for structures in distantly related taxa." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "deep genetic homology" + }, { + "pred" : "hasExactSynonym", + "val" : "deep homologous to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "generative homology" + }, { + "pred" : "hasRelatedSynonym", + "val" : "homoiology" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-05-26T08:41:07Z" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000044" } ] - }, - "type" : "PROPERTY", - "lbl" : "sends synaptic output to cell" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013008", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000045", + "lbl" : "in hemiplasy relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it.", - "xrefs" : [ ] + "val" : "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree.", + "xrefs" : [ "http://dx.doi.org/10.1073/pnas.0807433105", "http://purl.obolibrary.org/obo/HOM_0000045" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "hemiplasous to" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-1373-1705" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-05-26T08:40:18Z" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000045" } ] - }, - "type" : "PROPERTY", - "lbl" : "receives synaptic input from neuron" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0001199", - "type" : "CLASS", - "lbl" : "linear" - }, { - "id" : "http://purl.obolibrary.org/obo/UPHENO_0001001", - "type" : "CLASS", - "lbl" : "phenotype" - }, { - "id" : "http://purl.obolibrary.org/obo/OGMS_0000031", - "meta" : { - "definition" : { - "val" : "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "disease" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000060", - "meta" : { - "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], - "deprecated" : true - }, + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000046", + "lbl" : "in gametology relationship with", "type" : "PROPERTY", - "lbl" : "obsolete preceded by" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", "meta" : { "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", - "xrefs" : [ ] + "val" : "Historical homology that involves not recombining and subsequently differentiated sex chromosomes.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000046", "http://www.ncbi.nlm.nih.gov/pubmed/11110898" ] }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "gametologous to" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000046" } ] - }, - "type" : "PROPERTY", - "lbl" : "occurs in" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000047", + "lbl" : "in chromosomal homology relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t", - "xrefs" : [ ] + "val" : "Historical homology that involves the chromosomes able to pair (synapse) during meiosis.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000047", "ISBN:0195307615" ] }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "chromosomal homologous to" + } ], + "xrefs" : [ { + "val" : "MeSH:Chromosome_Pairing" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000047" } ] - }, - "type" : "PROPERTY", - "lbl" : "contains process" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000048", + "lbl" : "in many to many orthology relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", - "xrefs" : [ ] + "val" : "Orthology that involves two genes that experienced duplications more recent than the species split that created them.", + "xrefs" : [ "http://dx.doi.org/10.1038/415741a", "http://purl.obolibrary.org/obo/HOM_0000048", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/elements/1.1/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "many to many orthologous to" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + "pred" : "hasExactSynonym", + "val" : "many-to-many orthology" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" + "pred" : "hasExactSynonym", + "val" : "many:many orthology" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" + "pred" : "hasExactSynonym", + "val" : "trans-orthology" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" + "pred" : "hasRelatedSynonym", + "val" : "co-orthology" + }, { + "pred" : "hasRelatedSynonym", + "val" : "trans-homology" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000048" } ] - }, - "type" : "PROPERTY", - "lbl" : "preceded by" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000049", + "lbl" : "in within-species paralogy relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.", - "xrefs" : [ ] + "val" : "Paralogy that involves genes from the same species.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000049", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "within-species paralogous to" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000049" } ] - }, - "type" : "PROPERTY", - "lbl" : "precedes" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000019", - "type" : "CLASS", - "lbl" : "quality" + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000015", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000050", + "lbl" : "in between-species paralogy relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "process" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000016", - "type" : "CLASS", - "lbl" : "disposition" + "val" : "Paralogy that involves genes from different species.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000050", "http://www.ensembl.org/info/docs/compara/homology_method.html" ] + }, + "comments" : [ "The genes have diverged before a speciation event." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "between-species paralogous to" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000050" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000017", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000051", + "lbl" : "in postdisplacement relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "realizable entity" + "val" : "Paedomorphosis that is produced by delayed growth of immature structures into the adult form.", + "xrefs" : [ "http://en.wikipedia.org/wiki/Pedomorphosis", "http://purl.obolibrary.org/obo/HOM_0000051" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "post-displacement" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000051" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008508", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000052", + "lbl" : "in hypermorphosis relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "inverse of lays eggs on", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "has eggs laid on by" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008507", - "meta" : { - "definition" : { - "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "lays eggs on" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008506", - "meta" : { - "definition" : { - "val" : "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "ecologically co-occurs with" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008505", - "meta" : { - "definition" : { - "val" : "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism.", - "xrefs" : [ ] - } - }, - "type" : "PROPERTY", - "lbl" : "creates habitat for" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000004", - "meta" : { - "definition" : { - "val" : "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "independent continuant" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000006", - "type" : "CLASS", - "lbl" : "spatial region" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008504", - "meta" : { - "definition" : { - "val" : "inverse of kleptoparasite of", - "xrefs" : [ ] + "val" : "Peramorphosis that is produced by a delay in the offset of development.", + "xrefs" : [ "http://en.wikipedia.org/wiki/Peramorphosis", "http://purl.obolibrary.org/obo/HOM_0000052", "ISBN:978-0674639416" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, - "type" : "PROPERTY", - "lbl" : "kleptoparasitized by" + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000052" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008503", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000053", + "lbl" : "in synology relationship with", + "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material", - "xrefs" : [ ] + "val" : "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species.", + "xrefs" : [ "http://dx.doi.org/10.1007/BF00173425", "http://dx.doi.org/10.1016/S0168-9525(00)02005-9", "http://purl.obolibrary.org/obo/HOM_0000053" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "synologous to" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000053" } ] - }, - "type" : "PROPERTY", - "lbl" : "kleptoparasite of" + } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008502", - "meta" : { - "definition" : { - "val" : "inverse of epiphyte of", - "xrefs" : [ ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - }, + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000054", + "lbl" : "in isoorthology relationship with", "type" : "PROPERTY", - "lbl" : "has epiphyte" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0008501", "meta" : { "definition" : { - "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant.", - "xrefs" : [ ] + "val" : "Orthology that involves functional equivalent genes with retention of the ancestral function.", + "xrefs" : [ "http://dx.doi.org/10.1016/S0168-9525(00)02005-9", "http://purl.obolibrary.org/obo/HOM_0000054" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "isoorthologous to" + } ], + "xrefs" : [ { + "val" : "ECO:0000080" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Epiphyte" + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000054" } ] - }, - "type" : "PROPERTY", - "lbl" : "epiphyte of" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000051", - "type" : "CLASS", - "lbl" : "morphology" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0000052", - "type" : "CLASS", - "lbl" : "shape" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000002", - "meta" : { - "definition" : { - "val" : "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "continuant" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000003", - "meta" : { - "definition" : { - "val" : "An entity that has temporal parts and that happens, unfolds or develops through time.", - "xrefs" : [ ] - } - }, - "type" : "CLASS", - "lbl" : "occurrent" + } }, { - "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000055", + "lbl" : "in tandem paralogy relationship with", "type" : "PROPERTY", - "lbl" : "has_exact_synonym" - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0002009", - "type" : "CLASS", - "lbl" : "branchiness" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0016881", - "type" : "CLASS", - "lbl" : "acid-amino acid ligase activity" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000034", - "type" : "CLASS", - "lbl" : "function" - }, { - "id" : "http://purl.obolibrary.org/obo/ENVO_01000254", - "type" : "CLASS", - "lbl" : "environmental system" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000031", - "meta" : { - "definition" : { - "val" : "A continuant that is dependent on one or other independent continuant bearers. 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"chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002224", "http://purl.obolibrary.org/obo/RO_0002400" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002480", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002482", "http://purl.obolibrary.org/obo/RO_0002400" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002598", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002213" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002554", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002445", "http://purl.obolibrary.org/obo/RO_0002445" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004024", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002593", "http://purl.obolibrary.org/obo/BFO_0000050" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002110", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002110", "http://purl.obolibrary.org/obo/BFO_0000050" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002447", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002481", "http://purl.obolibrary.org/obo/RO_0002400" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002011", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002211", "http://purl.obolibrary.org/obo/RO_0002313" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000062" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000055", "http://purl.obolibrary.org/obo/RO_0000052" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013002", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0002162" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013003", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013003", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002211", "http://purl.obolibrary.org/obo/RO_0019000" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013007", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002211", "http://purl.obolibrary.org/obo/RO_0002025" ] + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0015001", "http://purl.obolibrary.org/obo/RO_0015003" ] } ] } ] } \ No newline at end of file diff --git a/ro.obo b/ro.obo index 1ce182cd..3d8e2e77 100644 --- a/ro.obo +++ b/ro.obo @@ -6,44 +6,28 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 60 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 310 Logical Axioms: 68] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 0 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 45 Logical Axioms: 10] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 3 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 104 Logical Axioms: 26] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] ontology: ro property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI property_value: owl:versionInfo "2023-02-19" xsd:string -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (first order logic expression)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (located in)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (gene product of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (differs in attribute of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (transcribed from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomal translation of)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (ribosomally translates to)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nSubClassOf( owl:Thing)\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nSubClassOf( owl:Thing)\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (material entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (immaterial entity)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: (ubiquitin-protein ligase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n# Class: (nucleus)\n\nSubClassOf( owl:Thing)\n\n# Class: (kinase activity)\n\nSubClassOf( ObjectHasSelf())\n\n# Class: ()\n\nSubClassOf( owl:Thing)\nSubClassOf( ObjectHasSelf())\n\n# Class: (cell projection)\n\nSubClassOf( owl:Thing)\n\n# Class: (synapse part)\n\nSubClassOf( owl:Thing)\n\n# Class: (sequentially ordered entity)\n\nSubClassOf( owl:Thing)\n\n# Class: owl:Nothing (owl:Nothing)\n\nSubClassOf(owl:Nothing owl:Nothing)\n\n# Class: ()\n\nSubClassOf( owl:Thing)\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\") Annotation(rdfs:label \"infer input from direct reg\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\") Annotation(rdfs:label \"involved in BP\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] id: BFO:0000002 name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] disjoint_from: BFO:0000003 ! occurrent -relationship: BFO:0000050 BFO:0000002 ! part of continuant -relationship: RO:0002214 BFO:0000002 ! has prototype continuant -relationship: RO:HOM0000000 BFO:0000002 ! continuant +relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant +relationship: RO:0002214 BFO:0000002 {all_only="true"} ! has prototype continuant +relationship: RO:HOM0000000 BFO:0000002 {all_only="true"} ! continuant [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: BFO:0000050 BFO:0000003 ! part of occurrent -relationship: RO:HOM0000000 BFO:0000003 ! occurrent +relationship: BFO:0000050 BFO:0000003 {all_only="true"} ! part of occurrent +relationship: RO:HOM0000000 BFO:0000003 {all_only="true"} ! occurrent [Term] id: BFO:0000004 @@ -52,7 +36,7 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000004 ! part of independent continuant +relationship: BFO:0000050 BFO:0000004 {all_only="true"} ! part of independent continuant [Term] id: BFO:0000006 @@ -64,7 +48,7 @@ id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] is_a: BFO:0000003 ! occurrent -relationship: RO:0002214 BFO:0000015 ! has prototype process +relationship: RO:0002214 BFO:0000015 {all_only="true"} ! has prototype process [Term] id: BFO:0000016 @@ -78,13 +62,13 @@ name: realizable entity def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality -relationship: BFO:0000050 BFO:0000017 ! part of realizable entity +relationship: BFO:0000050 BFO:0000017 {all_only="true"} ! part of realizable entity [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant -relationship: BFO:0000050 BFO:0000019 ! part of quality +relationship: BFO:0000050 BFO:0000019 {all_only="true"} ! part of quality [Term] id: BFO:0000020 @@ -92,7 +76,7 @@ name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant +relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant [Term] id: BFO:0000023 @@ -105,7 +89,7 @@ id: BFO:0000031 name: generically dependent continuant def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] is_a: BFO:0000002 ! continuant -relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant +relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant [Term] id: BFO:0000034 @@ -127,61 +111,50 @@ is_a: BFO:0000004 ! independent continuant [Term] id: CARO:0000000 name: anatomical entity -is_a: CARO:0030000 ! biological entity -property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl +def: "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." [CAROC:Brownsville2014] +comment: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. +is_a: BFO:0000004 ! independent continuant [Term] id: CARO:0000003 name: connected anatomical structure +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [] +comment: Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. is_a: CARO:0000006 ! material anatomical entity -property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl [Term] id: CARO:0000006 name: material anatomical entity -is_a: BFO:0000040 ! material entity +def: "An anatomical entity that has mass." [] is_a: CARO:0000000 ! anatomical entity -property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl +disjoint_from: CARO:0000007 ! immaterial anatomical entity [Term] id: CARO:0000007 name: immaterial anatomical entity +def: "Anatomical entity that has no mass." [] is_a: BFO:0000141 ! immaterial entity - -[Term] -id: CARO:0000011 -name: connected anatomical system -is_a: CARO:0010000 ! multicellular anatomical structure -is_a: RO:0002577 ! system - -[Term] -id: CARO:0001000 -name: multi-cell-part structure -is_a: CARO:0000003 ! connected anatomical structure -property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl +is_a: CARO:0000000 ! anatomical entity [Term] id: CARO:0001001 name: neuron projection bundle -is_a: CARO:0001000 ! multi-cell-part structure -property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl +def: "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." [] +is_a: CARO:0000006 ! material anatomical entity [Term] id: CARO:0001010 name: organism or virus or viroid +def: "Material anatomical entity that is a member of an individual species or is a viral or viroid particle." [] is_a: BFO:0000040 ! material entity +property_value: IAO:0000117 "Melissa Haendel" xsd:string [Term] id: CARO:0010000 name: multicellular anatomical structure +def: "An anatomical structure that has more than one cell as a part." [] is_a: CARO:0000003 ! connected anatomical structure -relationship: RO:0002207 CARO:0010000 ! directly develops from multicellular anatomical structure -property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl - -[Term] -id: CARO:0030000 -name: biological entity -is_a: BFO:0000004 ! independent continuant +property_value: IAO:0000117 "djs93" xsd:string [Term] id: CHEBI:50906 @@ -190,143 +163,234 @@ is_a: PATO:0000001 ! quality [Term] id: CL:0000000 name: cell -is_a: CARO:0000003 ! connected anatomical structure -relationship: RO:0002207 CL:0000000 ! directly develops from cell -property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl +def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] +comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). +xref: CALOHA:TS-2035 +xref: FBbt:00007002 +xref: FMA:68646 +xref: GO:0005623 +xref: KUPO:0000002 +xref: MESH:D002477 +xref: VHOG:0001533 +xref: WBbt:0004017 +xref: XAO:0003012 + +[Term] +id: CL:0000101 +name: sensory neuron +def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] +xref: BTO:0001037 +xref: FBbt:00005124 +xref: FMA:84649 +xref: MESH:D011984 +xref: WBbt:0005759 +is_a: CL:0000540 ! neuron [Term] id: CL:0000540 name: neuron +def: "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [http://en.wikipedia.org/wiki/Neuron, MESH:D009474] +comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. +synonym: "nerve cell" EXACT [] +xref: BTO:0000938 +xref: CALOHA:TS-0683 +xref: FBbt:00005106 +xref: FMA:54527 +xref: VHOG:0001483 +xref: WBbt:0003679 +is_a: BFO:0000040 ! material entity is_a: CL:0000000 ! cell -property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl - -[Term] -id: ENVO:00000428 -name: biome -is_a: ENVO:01000254 ! environmental system +property_value: RO:0002175 NCBITaxon:9606 [Term] id: ENVO:01000254 name: environmental system +def: "A system which has the disposition to environ one or more material entities." [DOI:10.1186/2041-1480-4-43] +comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. +synonym: "environment" EXACT [] +xref: EcoLexicon:environment is_a: RO:0002577 ! system +creation_date: 2013-09-23T16:04:08Z [Term] id: GO:0003674 name: molecular_function -is_a: BFO:0000015 ! process -property_value: IAO:0000589 "molecular process" xsd:string - -[Term] -id: GO:0003824 -name: catalytic activity -is_a: GO:0003674 ! molecular_function +def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [GOC:pdt] +comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. +synonym: "molecular function" EXACT [] [Term] id: GO:0004842 -name: ubiquitin-protein ligase activity -is_a: GO:0019787 ! small conjugating protein ligase activity +name: ubiquitin-protein transferase activity +def: "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." [GOC:BioGRID, GOC:jh2, PMID:9635407] +synonym: "anaphase-promoting complex activity" NARROW [GOC:dph, GOC:tb] +synonym: "E2" RELATED [] +synonym: "E3" RELATED [] +synonym: "ubiquitin conjugating enzyme activity" NARROW [] +synonym: "ubiquitin ligase activity" NARROW [] +synonym: "ubiquitin protein ligase activity" NARROW [] +synonym: "ubiquitin protein-ligase activity" NARROW [] +synonym: "ubiquitin-conjugating enzyme activity" NARROW [] +xref: KEGG_REACTION:R03876 +xref: Reactome:R-HSA-1169394 "ISGylation of IRF3" +xref: Reactome:R-HSA-1169395 "ISGylation of viral protein NS1" +xref: Reactome:R-HSA-1169397 "Activation of ISG15 by UBA7 E1 ligase" +xref: Reactome:R-HSA-1169398 "ISGylation of host protein filamin B" +xref: Reactome:R-HSA-1169402 "ISGylation of E2 conjugating enzymes" +xref: Reactome:R-HSA-1169405 "ISGylation of protein phosphatase 1 beta (PP2CB)" +xref: Reactome:R-HSA-1169406 "ISGylation of host proteins" +xref: Reactome:R-HSA-1234163 "Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha" +xref: Reactome:R-HSA-1234172 "Nuclear VBC complex ubiquitinylates HIF-alpha" +xref: Reactome:R-HSA-1253282 "ERBB4 ubiquitination by WWP1/ITCH" +xref: Reactome:R-HSA-1358789 "Self-ubiquitination of RNF41" +xref: Reactome:R-HSA-1358790 "RNF41 ubiquitinates ERBB3" +xref: Reactome:R-HSA-1358792 "RNF41 ubiquitinates activated ERBB3" +xref: Reactome:R-HSA-1363331 "Ubiquitination of p130 (RBL2) by SCF (Skp2)" +xref: Reactome:R-HSA-168915 "K63-linked ubiquitination of RIP1 bound to the activated TLR complex" +xref: Reactome:R-HSA-173542 "SMURF2 ubiquitinates SMAD2" +xref: Reactome:R-HSA-173545 "Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling" +xref: Reactome:R-HSA-174057 "Multiubiquitination of APC/C-associated Cdh1" +xref: Reactome:R-HSA-174104 "Ubiquitination of Cyclin A by APC/C:Cdc20 complex" +xref: Reactome:R-HSA-174144 "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex" +xref: Reactome:R-HSA-174159 "Ubiquitination of Emi1 by SCF-beta-TrCP" +xref: Reactome:R-HSA-174195 "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex" +xref: Reactome:R-HSA-174227 "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex" +xref: Reactome:R-HSA-179417 "Multiubiquitination of Nek2A" +xref: Reactome:R-HSA-180540 "Multi-ubiquitination of APOBEC3G" +xref: Reactome:R-HSA-180597 "Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex" +xref: Reactome:R-HSA-182986 "CBL-mediated ubiquitination of CIN85" +xref: Reactome:R-HSA-182993 "Ubiquitination of stimulated EGFR (CBL)" +xref: Reactome:R-HSA-183036 "Ubiquitination of stimulated EGFR (CBL:GRB2)" +xref: Reactome:R-HSA-183051 "CBL ubiquitinates Sprouty" +xref: Reactome:R-HSA-183084 "CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix" +xref: Reactome:R-HSA-183089 "CBL binds and ubiquitinates phosphorylated Sprouty" +xref: Reactome:R-HSA-1852623 "Ubiquitination of NICD1 by FBWX7" +xref: Reactome:R-HSA-187575 "Ubiquitination of phospho-p27/p21" +xref: Reactome:R-HSA-1912357 "ITCH ubiquitinates DTX" +xref: Reactome:R-HSA-1912386 "Ubiquitination of NOTCH1 by ITCH in the absence of ligand" +xref: Reactome:R-HSA-1918092 "CHIP (STUB1) mediates ubiquitination of ERBB2" +xref: Reactome:R-HSA-1918095 "CUL5 mediates ubiquitination of ERBB2" +xref: Reactome:R-HSA-1977296 "NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer" +xref: Reactome:R-HSA-1980074 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1" +xref: Reactome:R-HSA-1980118 "ARRB mediates NOTCH1 ubiquitination" +xref: Reactome:R-HSA-201425 "Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling" +xref: Reactome:R-HSA-202453 "Auto-ubiquitination of TRAF6" +xref: Reactome:R-HSA-202534 "Ubiquitination of NEMO by TRAF6" +xref: Reactome:R-HSA-205118 "TRAF6 polyubiquitinates NRIF" +xref: Reactome:R-HSA-209063 "Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex" +xref: Reactome:R-HSA-211734 "Ubiquitination of PAK-2p34" +xref: Reactome:R-HSA-2169050 "SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7" +xref: Reactome:R-HSA-2172172 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH2" +xref: Reactome:R-HSA-2179276 "SMURF2 monoubiquitinates SMAD3" +xref: Reactome:R-HSA-2186747 "Ubiquitination of SKI/SKIL by RNF111/SMURF2" +xref: Reactome:R-HSA-2186785 "RNF111 ubiquitinates SMAD7" +xref: Reactome:R-HSA-2187368 "STUB1 (CHIP) ubiquitinates SMAD3" +xref: Reactome:R-HSA-2213017 "Auto-ubiquitination of TRAF3" +xref: Reactome:R-HSA-264444 "Autoubiquitination of phospho-COP1(Ser-387 )" +xref: Reactome:R-HSA-2682349 "RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels" +xref: Reactome:R-HSA-2730904 "Auto-ubiquitination of TRAF6" +xref: Reactome:R-HSA-2737728 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants" +xref: Reactome:R-HSA-2769007 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants" +xref: Reactome:R-HSA-2900765 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants" +xref: Reactome:R-HSA-3000335 "SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA" +xref: Reactome:R-HSA-3134804 "STING ubiquitination by TRIM32 or TRIM56" +xref: Reactome:R-HSA-3134946 "DDX41 ubiquitination by TRIM21" +xref: Reactome:R-HSA-3249386 "DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1" +xref: Reactome:R-HSA-3780995 "NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2" +xref: Reactome:R-HSA-3781009 "NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1" +xref: Reactome:R-HSA-3788724 "Cdh1:APC/C ubiquitinates EHMT1 and EHMT2" +xref: Reactome:R-HSA-3797226 "Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease)" +xref: Reactome:R-HSA-400267 "BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins" +xref: Reactome:R-HSA-4332236 "CBL neddylates TGFBR2" +xref: Reactome:R-HSA-446877 "TRAF6 is K63 poly-ubiquitinated" +xref: Reactome:R-HSA-450358 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation" +xref: Reactome:R-HSA-451418 "Pellino ubiquitinates IRAK1" +xref: Reactome:R-HSA-5205682 "Parkin promotes the ubiquitination of mitochondrial substrates" +xref: Reactome:R-HSA-5357757 "BIRC(cIAP1/2) ubiquitinates RIPK1" +xref: Reactome:R-HSA-5362412 "SYVN1 ubiquitinates Hh C-terminal fragments" +xref: Reactome:R-HSA-5483238 "Hh processing variants are ubiquitinated" +xref: Reactome:R-HSA-5607725 "SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP" +xref: Reactome:R-HSA-5607728 "beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex" +xref: Reactome:R-HSA-5607756 "TRAF6 oligomer autoubiquitinates" +xref: Reactome:R-HSA-5607757 "K63polyUb-TRAF6 ubiquitinates TAK1" +xref: Reactome:R-HSA-5610742 "SCF(beta-TrCP) ubiquitinates p-GLI1" +xref: Reactome:R-HSA-5610745 "SCF(beta-TrCP) ubiquitinates p-GLI2" +xref: Reactome:R-HSA-5610746 "SCF(beta-TrCP) ubiquitinates p-GLI3" +xref: Reactome:R-HSA-5652009 "RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA" +xref: Reactome:R-HSA-5655170 "RCHY1 monoubiquitinates POLH" +xref: Reactome:R-HSA-5660753 "SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA" +xref: Reactome:R-HSA-5667107 "SIAH1, SIAH2 ubiquitinate SNCAIP" +xref: Reactome:R-HSA-5667111 "PARK2 K63-Ubiquitinates SNCAIP" +xref: Reactome:R-HSA-5668454 "K63polyUb-cIAP1,2 ubiquitinates TRAF3" +xref: Reactome:R-HSA-5668534 "cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK" +xref: Reactome:R-HSA-5675470 "BIRC2/3 (cIAP1/2) is autoubiquitinated" +xref: Reactome:R-HSA-5684250 "SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2" +xref: Reactome:R-HSA-5691108 "SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2" +xref: Reactome:R-HSA-5693108 "TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains" +xref: Reactome:R-HSA-69598 "Ubiquitination of phosphorylated Cdc25A" +xref: Reactome:R-HSA-741386 "RIP2 induces K63-linked ubiquitination of NEMO" +xref: Reactome:R-HSA-75824 "Ubiquitination of Cyclin D1" +xref: Reactome:R-HSA-870449 "TRIM33 monoubiquitinates SMAD4" +xref: Reactome:R-HSA-8948709 "DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3" +xref: Reactome:R-HSA-8956106 "VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha" +xref: Reactome:R-HSA-9013069 "Ubiquitination of DLL/JAG ligands upon binding to NOTCH3" +xref: Reactome:R-HSA-9013974 "Auto-ubiquitination of TRAF3 within activated TLR3 complex" +xref: Reactome:R-HSA-9014342 "K63-linked ubiquitination of RIP1 bound to the activated TLR complex" +xref: Reactome:R-HSA-918224 "DDX58 is K63 polyubiquitinated" +xref: Reactome:R-HSA-936412 "RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS" +xref: Reactome:R-HSA-936942 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2" +xref: Reactome:R-HSA-936986 "Activated TRAF6 synthesizes unanchored polyubiquitin chains" +xref: Reactome:R-HSA-9628444 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation" +xref: Reactome:R-HSA-9645394 "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation" +xref: Reactome:R-HSA-9645414 "Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer" +xref: Reactome:R-HSA-9688831 "STUB1 ubiquitinates RIPK3 at K55, K363" +xref: Reactome:R-HSA-9701000 "BRCA1:BARD1 heterodimer autoubiquitinates" +xref: Reactome:R-HSA-975118 "TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex" +xref: Reactome:R-HSA-975147 "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane" +xref: Reactome:R-HSA-983140 "Transfer of Ub from E2 to substrate and release of E2" +xref: Reactome:R-HSA-983153 "E1 mediated ubiquitin activation" +xref: Reactome:R-HSA-983156 "Polyubiquitination of substrate" +is_a: GO:0003674 ! molecular_function [Term] id: GO:0005634 name: nucleus -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl +def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GOC:go_curators] +synonym: "cell nucleus" EXACT [] +synonym: "horsetail nucleus" NARROW [GOC:al, GOC:mah, GOC:vw, PMID:15030757] +xref: NIF_Subcellular:sao1702920020 +xref: Wikipedia:Cell_nucleus [Term] id: GO:0008150 name: biological_process -is_a: BFO:0000015 ! process - -[Term] -id: GO:0016020 -name: membrane -is_a: CARO:0000003 ! connected anatomical structure -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl +def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +created_by: jl +creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0016301 name: kinase activity -is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups - -[Term] -id: GO:0016740 -name: transferase activity -is_a: GO:0003824 ! catalytic activity - -[Term] -id: GO:0016772 -name: transferase activity, transferring phosphorus-containing groups -is_a: GO:0016740 ! transferase activity - -[Term] -id: GO:0016874 -name: ligase activity -is_a: GO:0003824 ! catalytic activity - -[Term] -id: GO:0016879 -name: ligase activity, forming carbon-nitrogen bonds -is_a: GO:0016874 ! ligase activity - -[Term] -id: GO:0016881 -name: acid-amino acid ligase activity -is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds +def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [ISBN:0198506732] +comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. +synonym: "phosphokinase activity" EXACT [] +xref: Reactome:R-HSA-6788855 "FN3KRP phosphorylates PsiAm, RibAm" +xref: Reactome:R-HSA-6788867 "FN3K phosphorylates ketosamines" +is_a: GO:0003674 ! molecular_function [Term] id: GO:0019107 - -[Term] -id: GO:0019787 -name: small conjugating protein ligase activity -is_a: GO:0016881 ! acid-amino acid ligase activity - -[Term] -id: GO:0030424 -name: axon -is_a: GO:0043005 ! neuron projection -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0030425 -name: dendrite -is_a: GO:0043005 ! neuron projection -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0042734 -name: presynaptic membrane -is_a: GO:0016020 ! membrane -is_a: GO:0044456 ! synapse part -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0042995 -name: cell projection -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0043005 -name: neuron projection -is_a: GO:0042995 ! cell projection -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0044456 -name: synapse part -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0045202 -name: synapse -is_a: CARO:0000003 ! connected anatomical structure -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl - -[Term] -id: GO:0045211 -name: postsynaptic membrane -is_a: GO:0016020 ! membrane -is_a: GO:0044456 ! synapse part -property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl +name: myristoyltransferase activity +def: "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule." [GOC:ai] +xref: Reactome:R-HSA-141367 "Myristoylation of tBID by NMT1" +xref: Reactome:R-HSA-162914 "Myristoylation of Nef" +is_a: GO:0003674 ! molecular_function [Term] id: OGMS:0000031 @@ -337,49 +401,31 @@ is_a: BFO:0000016 ! disposition [Term] id: PATO:0000001 name: quality +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] is_a: BFO:0000020 ! specifically dependent continuant -property_value: IAO:0000589 "quality (PATO)" xsd:string - -[Term] -id: PATO:0000051 -name: morphology -is_a: BFO:0000019 ! quality -is_a: PATO:0001241 ! physical object quality - -[Term] -id: PATO:0000052 -name: shape -is_a: PATO:0000051 ! morphology - -[Term] -id: PATO:0000141 -name: structure -is_a: PATO:0000051 ! morphology [Term] id: PATO:0000402 name: branched -is_a: PATO:0002009 ! branchiness +def: "A branchiness quality inhering in a bearer by virtue of the bearer's having branches." [WordNet:WordNet] +synonym: "ramified" EXACT [] +synonym: "ramiform" EXACT [] +is_a: PATO:0000001 ! quality +property_value: RO:0002604 PATO:0000414 [Term] id: PATO:0001199 name: linear -is_a: PATO:0000052 ! shape - -[Term] -id: PATO:0001241 -name: physical object quality +def: "A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel." [ISBN:0881923214] is_a: PATO:0000001 ! quality -[Term] -id: PATO:0002009 -name: branchiness -is_a: PATO:0000052 ! shape - [Term] id: PATO:0002124 name: laminar -is_a: PATO:0000141 ! structure +def: "A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer." [PATOC:GVG] +is_a: PATO:0000001 ! quality +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +creation_date: 2009-10-06T04:37:14Z [Term] id: RO:0002310 @@ -390,7 +436,7 @@ property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-660 property_value: IAO:0000112 "An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human," xsd:string property_value: IAO:0000112 "An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes." xsd:anyURI property_value: IAO:0000116 "This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/pull/173 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/pull/173" xsd:anyURI created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-06-05T17:55:39Z @@ -424,7 +470,7 @@ def: "A material entity consisting of multiple components that are causally inte is_a: BFO:0000040 ! material entity property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string +property_value: IAO:0000119 "http://www.jbiomedsem.com/content/4/1/43" xsd:string [Term] id: UPHENO:0001001 @@ -457,7 +503,7 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf -property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string is_transitive: true is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part @@ -522,7 +568,7 @@ id: BFO:0000062 name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string @@ -576,6 +622,11 @@ comment: Paraphrase of definition: a relation between an independent continuant property_value: IAO:0000111 "site of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +[Typedef] +id: ENVO:01003004 +name: derives from part of +def: "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." [] + [Typedef] id: RO:0000052 name: characteristic of @@ -621,7 +672,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -869,7 +920,7 @@ id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string @@ -942,7 +993,7 @@ is_a: RO:0001018 ! contained in [Typedef] id: RO:0002005 name: innervated_by -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI +property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 domain: CARO:0000003 ! connected anatomical structure range: CARO:0001001 ! neuron projection bundle @@ -1573,7 +1624,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_symmetric: true @@ -1679,7 +1730,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -1689,8 +1740,8 @@ name: connected to def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -1700,8 +1751,8 @@ def: "c connects a if and only if there exist some b such that a and b are simil property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 ! independent continuant is_a: RO:0002323 ! mereotopologically related to @@ -2031,7 +2082,7 @@ id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra @@ -2211,28 +2262,28 @@ is_a: RO:0000057 ! has participant id: RO:0002240 name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002241 name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: RO:0002309 ! has exposure stimulus [Typedef] id: RO:0002242 name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002243 name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: RO:0002244 ! related via exposure to [Typedef] @@ -2327,7 +2378,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 ! material anatomical entity @@ -2473,7 +2524,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2487,7 +2538,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -2503,7 +2554,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2518,7 +2569,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2638,7 +2689,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 ! connected anatomical structure is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -2990,7 +3041,7 @@ is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps @@ -3010,7 +3061,7 @@ id: RO:0002372 name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! connected anatomical structure is_a: RO:0002371 ! attached to @@ -3021,7 +3072,7 @@ id: RO:0002373 name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! connected anatomical structure is_a: RO:0002371 ! attached to @@ -3049,7 +3100,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002323 ! mereotopologically related to @@ -3066,11 +3117,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with @@ -3085,7 +3136,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with @@ -3117,7 +3168,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 holds_over_chain: RO:0002377 RO:0002381 is_a: BFO:0000050 ! part of @@ -3369,7 +3420,7 @@ name: differs in comment: This is an exploratory relation property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions xsd:anyURI +property_value: seeAlso "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" xsd:anyURI [Typedef] id: RO:0002425 @@ -3460,12 +3511,12 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true @@ -3473,7 +3524,7 @@ is_symmetric: true [Typedef] id: RO:0002435 name: genetically interacts with -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 @@ -3484,7 +3535,7 @@ is_a: RO:0002434 ! interacts with id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3500,7 +3551,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true @@ -3528,8 +3579,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002458 ! preyed upon by @@ -3539,7 +3590,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -3550,7 +3601,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -3559,7 +3610,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -3568,7 +3619,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -3580,7 +3631,7 @@ synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002454 ! has host inverse_of: RO:0002445 ! parasitized by @@ -3593,7 +3644,7 @@ synonym: "directly parasitized by" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002453 ! host of @@ -3683,7 +3734,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -3694,7 +3745,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: RO:0002442 ! mutualistically interacts with inverse_of: RO:0002456 ! pollinated by @@ -3705,7 +3756,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: RO:0002442 ! mutualistically interacts with [Typedef] @@ -3726,8 +3777,8 @@ subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: RO:0002438 ! trophically interacts with [Typedef] @@ -4120,7 +4171,7 @@ id: RO:0002510 name: transcribed from def: "x is transcribed from y if and only if x is synthesized from template y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002511 ! transcribed to @@ -4130,7 +4181,7 @@ name: transcribed to def: "inverse of transcribed from" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to [Typedef] @@ -4138,7 +4189,7 @@ id: RO:0002512 name: ribosomal translation of def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002513 ! ribosomally translates to @@ -4147,7 +4198,7 @@ id: RO:0002513 name: ribosomally translates to def: "inverse of ribosomal translation of" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to [Typedef] @@ -4156,7 +4207,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 ! sequentially ordered entity @@ -4171,7 +4222,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002527 ! does not overlap sequence of [Typedef] @@ -4182,7 +4233,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002524 ! has subsequence inverse_of: RO:0002517 ! is start sequence of @@ -4195,7 +4246,7 @@ subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002525 ! is subsequence of @@ -4207,7 +4258,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002524 ! has subsequence inverse_of: RO:0002519 ! is end sequence of @@ -4220,7 +4271,7 @@ subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002525 ! is subsequence of @@ -4231,7 +4282,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002524 ! has subsequence [Typedef] @@ -4272,7 +4323,7 @@ def: "x has subsequence y iff all of the sequence parts of y are sequence parts property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: BFO:0000051 ! has part is_a: RO:0002522 ! bounds sequence of @@ -4384,8 +4435,8 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string holds_over_chain: RO:0002444 RO:0002444 is_a: RO:0002454 ! has host inverse_of: RO:0002554 ! hyperparasitized by @@ -4408,8 +4459,8 @@ id: RO:0002555 name: allelopath of subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -4453,7 +4504,7 @@ id: RO:0002563 name: interaction relation helper property property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] @@ -4500,7 +4551,7 @@ id: RO:0002568 name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: RO:0002567 ! biomechanically related to [Typedef] @@ -4520,7 +4571,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -4532,7 +4583,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 ! material entity is_a: BFO:0000050 ! part of @@ -4777,7 +4828,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping [Typedef] id: RO:0002618 name: visits -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002619 ! visited by @@ -4813,7 +4864,7 @@ is_a: RO:0002619 ! visited by [Typedef] id: RO:0002626 name: kills -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002627 ! is killed by @@ -4852,7 +4903,7 @@ is_a: RO:0002578 ! directly regulates id: RO:0002632 name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002444 ! parasite of inverse_of: RO:0002633 ! has ectoparasite @@ -4868,7 +4919,7 @@ id: RO:0002634 name: endoparasite of synonym: "lives inside of" RELATED [] property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002444 ! parasite of inverse_of: RO:0002635 ! has endoparasite @@ -4895,7 +4946,7 @@ is_a: RO:0002445 ! parasitized by id: RO:0002638 name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002639 ! has intercellular endoparasite @@ -4910,7 +4961,7 @@ is_a: RO:0002635 ! has endoparasite id: RO:0002640 name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002641 ! has intracellular endoparasite @@ -5443,7 +5494,7 @@ is_a: RO:0007000 ! has driver id: RO:0008501 name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: RO:0002440 ! symbiotically interacts with inverse_of: RO:0008502 ! has epiphyte @@ -5458,7 +5509,7 @@ is_a: RO:0002440 ! symbiotically interacts with id: RO:0008503 name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: RO:0002444 ! parasite of inverse_of: RO:0008504 ! kleptoparasitized by @@ -5561,7 +5612,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 ! realizable entity range: BFO:0000015 ! process holds_over_chain: BFO:0000054 RO:0002404 @@ -5906,7 +5957,7 @@ def: "Relation between a sensory neuron and some structure in which it receives synonym: "has sensory dendrite location" EXACT [] synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] -domain: CL:0000101 +domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location transitive_over: BFO:0000050 ! part of created_by: http://orcid.org/0000-0002-1373-1705 @@ -6046,25 +6097,25 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0016001 name: has phenotype or disease property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease [Typedef] id: RO:0016004 name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: RO:0002244 ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 diff --git a/ro.owl b/ro.owl index e1982ee4..9a8a8f42 100644 --- a/ro.owl +++ b/ro.owl @@ -8,6 +8,7 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:cito="http://purl.org/spar/cito/" + xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" @@ -15,23 +16,11 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" + xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - - - - - - - - - - - The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology @@ -52,9 +41,59 @@ + + + + + + + + + + + + + + + + + + + + + + + + - + + definition + + + + + + + + + + + + + + + + + + + + + + + + + @@ -64,40 +103,100 @@ + + + + + + + + + + + + + + + + + + - + An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. - + - + + + OBO foundry unique label + + + + + + + + + + + + + - + + + term replaced by + - + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + defined by construct + - + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + temporal interpretation - + @@ -864,6 +963,18 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -882,6 +993,18 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -936,6 +1059,18 @@ Where we have an annotation assertion + + + + + + + + + + + + @@ -956,12 +1091,42 @@ Where we have an annotation assertion + + + + + + + + + + has_broad_synonym + + + + + + + + database_cross_reference + + + + + + + + has_exact_synonym + + + + @@ -970,6 +1135,28 @@ Where we have an annotation assertion + + + + has_obo_format_version + + + + + + + + has_related_synonym + + + + + + + + + + @@ -984,6 +1171,32 @@ Where we have an annotation assertion + + + + + + + + + + is defined by + + + + + is defined by + This is an experimental annotation + + + + + + + + + + @@ -996,6 +1209,12 @@ Where we have an annotation assertion + + + + + + + + + + + + realized in + this disease is realized in this disease course + this fragility is realized in this shattering + this investigator role is realized in this investigation + is realized by + realized_in + [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + + + realizes + this disease course realizes this disease + this investigation realizes this investigator role + this shattering realizes this fragility + to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + accidentally included in BFO 1.2 proposal + - should have been BFO_0000062 + obsolete preceded by + true - + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by - + preceded by + - + + + + @@ -1063,32 +1384,122 @@ Where we have an annotation assertion + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - + precedes + - + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in - + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity. + derives from part of + - + - + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + has characteristic + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + - + + + @@ -1098,38 +1509,192 @@ Where we have an annotation assertion - + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + - + - - - - OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. - - - - Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). - obsolete in neural circuit with - true + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as - + - - - - OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. - - - - Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). - obsolete upstream in neural circuit with - true + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + + + + + + + OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete in neural circuit with + true + + + + + + + + + + OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete upstream in neural circuit with + true @@ -1150,6 +1715,55 @@ Where we have an annotation assertion + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + + derives from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + + derives into + + + + + + + + + + is location of + my head is the location of my brain + this cage is the location of this rat + a relation between two independent continuants, the location and the target, in which the target is entirely within the location + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + location_of + + location of + + + + @@ -1236,22 +1850,78 @@ range: spatial region or site (immaterial continuant) - + + + + + + + + + + + + + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in - + located in + + + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. + + + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. + - + + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of - + + 2D boundary of + @@ -1270,10 +1940,20 @@ range: spatial region or site (immaterial continuant) - + + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - + has boundary + has_2D_boundary + + has 2D boundary + @@ -1682,12 +2362,56 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + + Primitive instance level timing relation between events + before or simultaneous with + + + + - + + + + David Osumi-Sutherland - + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + @@ -1705,56 +2429,134 @@ Examples include: the relationship between two channels collected simultaneously + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + - + + + - + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + - + + + + David Osumi-Sutherland - + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + + + + + David Osumi-Sutherland + + starts before + - + + + David Osumi-Sutherland + ends_at_start_of + meets - + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + - + + + + + David Osumi-Sutherland + io - + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + - + + + + David Osumi-Sutherland + d + during - + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + @@ -3066,31 +3868,52 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to - + + + + + inverse of starts with + Chris Mungall + Allen - + starts + - + + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by - + starts with + @@ -3151,21 +3974,34 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + + + + + inverse of ends with + Chris Mungall - + ends + - + + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by - + ends with + @@ -3521,19 +4357,31 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + has biological role + - + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + has application role + - + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + has chemical role + @@ -4350,6 +5198,35 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + @@ -7871,10 +8748,10 @@ Environmental exposures include those imposed by natural environments, experimen p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - GOC:kva - GOC:pt GOC:cjm GOC:dph + GOC:kva + GOC:pt PMID:27812932 @@ -7895,10 +8772,10 @@ Environmental exposures include those imposed by natural environments, experimen p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - GOC:kva - GOC:pt GOC:cjm GOC:dph + GOC:kva + GOC:pt PMID:27812932 @@ -8352,13 +9229,32 @@ Environmental exposures include those imposed by natural environments, experimen - + - - A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity. - - has driver - + + DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. + DEPRECATED inheres in + true + + + + + + + + DEPRECATED bearer of + true + + + + + + + + A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity. + + has driver + @@ -9558,632 +10454,3198 @@ For example, protein A (transcription factor) indirectly increases by expression - + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. TODO: Add homeomorphy axiom - + + + ECO:0000041 + SO:similar_to + sameness + similar to + correspondence + resemblance + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + - + - + + + + Similarity that results from common evolutionary origin. + + + homologous to + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + + + + + + + + + + + + + Similarity that results from independent evolution. + + + homoplasous to + analogy + in homoplasy relationship with + + + + + + Similarity that results from independent evolution. + + + - + - + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + ECO:0000075 + homocracous to + Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + in homocracy relationship with + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + + + - + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + analogy + Convergence usually implies a notion of adaptation. + in convergence relationship with + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + - + - - - - - - - 0 - - - 100 - - - - - Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - dos - 2018-05-22T16:43:28Z - This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. - has increased age-specific mortality rate - + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + parallel evolution + Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + in parallelism relationship with + + - + - Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - PMID:24138933 - Wikipedia:Infant_mortality + Homoplasy that involves homologous underlying mechanisms or structures. + + - + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + ECO:0000071 + MI:2163 + structural homologous to + idealistic homology + in structural homology relationship with + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + + ISBN:0123195837 + - + - - - - - - - - - - - - - - - + + + + Homology that is defined by common descent. + + + homology + ECO:0000080 + RO_proposed_relation:homologous_to + SO:0000330 + SO:0000853 + SO:0000857 + SO:homologous_to + TAO:homologous_to + cladistic homology + historical homologous to + phylogenetic homology + taxic homology + true homology + in historical homology relationship with + + + + + + Homology that is defined by common descent. + + + ISBN:0123195837 + - + - - - - - - - - - + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + ECO:0000067 + biological homologous to + transformational homology + Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + in biological homology relationship with + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + + - + - - - + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + atavism + rudiment + reversion + in reversal relationship with + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + - + - - - + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + + MeSH:Synteny + SO:0000860 + SO:0005858 + syntenic homologous to + synteny + in syntenic homology relationship with + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + MeSH:Synteny + - + - - - - - - - - - + + + + + Historical homology that involves genes that diverged after a duplication event. + + + SO:0000854 + SO:0000859 + SO:paralogous_to + paralogous to + in paralogy relationship with + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + + + - + - - - + + + + + Paralogy that involves sets of syntenic blocks. + + + syntenic paralogous to + duplicon + paralogon + in syntenic paralogy relationship with + + + + + + Paralogy that involves sets of syntenic blocks. + + + DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y + - + - - - + + + + Syntenic homology that involves chromosomes of different species. + + + syntenic orthologous to + in syntenic orthology relationship with + + + + + + Syntenic homology that involves chromosomes of different species. + + + - + - - - + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + + fractional homology + partial homologous to + segmental homology + mixed homology + modular homology + partial correspondence + percent homology + in partial homology relationship with + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + ISBN:0123195837 + ISBN:978-0471984931 + - + - - - + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + MeSH:Structural_Homology,_Protein + protein structural homologous to + in protein structural homology relationship with + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + - + - - - + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + + pseudogene + SO:non_functional_homolog_of + non functional homologous to + in non functional homology relationship with + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + SO:non_functional_homolog_of + - + - - - + + + + Historical homology that involves genes that diverged after a speciation event. + + + ECO:00000060 + SO:0000855 + SO:0000858 + SO:orthologous_to + orthologous to + The term is sometimes also used for anatomical structures. + in orthology relationship with + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + + + + - + - - - + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + xenologous to + The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + in xenology relationship with + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + + - + - - - + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + + 1 to 1 homologous to + 1:1 homology + one-to-one homology + in 1 to 1 homology relationship with + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + BGEE:curator + - + - - - + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + 1 to 1 orthologous to + 1:1 orthology + one-to-one orthology + in 1 to 1 orthology relationship with + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + + - + - - - + + + + Paralogy that results from a whole genome duplication event. + + + ohnologous to + homoeology + in ohnology relationship with + + + + + + Paralogy that results from a whole genome duplication event. + + + - + - - - + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + in-paralogous to + inparalogy + symparalogy + in in-paralogy relationship with + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + - + - - - - + + + + Paralogy that results from a duplication preceding a given speciation event. + + + alloparalogy + out-paralogous to + outparalogy + in out-paralogy relationship with + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + - + - - - + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + pro-orthologous to + in pro-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + + - + - - - - + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + semi-orthologous to + The converse of pro-orthologous. + in semi-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + + - + - - - + + + + Iterative homology that involves structures arranged along the main body axis. + + + serial homologous to + homonomy + in serial homology relationship with + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + - + - - - + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + + heterochronous homologous to + heterochrony + in heterochronous homology relationship with + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + ISBN:978-0674639416 + - + - - - + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + juvenification + pedomorphosis + in paedomorphorsis relationship with + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + ISBN:978-0674639416 + - + - - - + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + in peramorphosis relationship with + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + - + - - - + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + in progenesis relationship with + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + ISBN:978-0674639416 + - + - - - + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + juvenilization + neotenous to + in neoteny relationship with + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + ISBN:978-0674639416 + - + - - - + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + mimicrous to + in mimicry relationship with + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + - + - - - + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + 1 to many orthologous to + 1:many orthology + one-to-many orthology + co-orthology + many to 1 orthology + in 1 to many orthology relationship with + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + + - + - - - + + + + Historical homology that involves two members of a larger set of homologs. + + + many to many homologous to + many-to-many homology + many:many homology + in many to many homology relationship with + + + + + + Historical homology that involves two members of a larger set of homologs. + + + - + - - - + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + + 1 to many homologous to + one-to-many homology + 1:many homology + in 1 to many homology relationship with + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + BGEE:curator + - + - - - + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + + apomorphous to + synapomorphy + in apomorphy relationship with + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + ISBN:978-0252068140 + - + - - - + + + + Historical homology that is based on distant shared ancestry. + + + plesiomorphous to + symplesiomorphy + This term is usually contrasted to apomorphy. + in plesiomorphy relationship with + + + + + + Historical homology that is based on distant shared ancestry. + + ISBN:978-0252068140 + - + - - - + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + deep genetic homology + deep homologous to + generative homology + homoiology + Used for structures in distantly related taxa. + in deep homology relationship with + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + + - + - - - - - - true - - - + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + hemiplasous to + in hemiplasy relationship with + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + - + - - - + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + gametologous to + in gametology relationship with + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + - + - - - + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + + MeSH:Chromosome_Pairing + chromosomal homologous to + in chromosomal homology relationship with + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + ISBN:0195307615 + - + - - - + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + many to many orthologous to + many-to-many orthology + many:many orthology + trans-orthology + co-orthology + trans-homology + in many to many orthology relationship with + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + + - + - - - + + + + + Paralogy that involves genes from the same species. + + + within-species paralogous to + in within-species paralogy relationship with + + + + + + Paralogy that involves genes from the same species. + + + - + - - - - - - true - - - + + + + Paralogy that involves genes from different species. + + + between-species paralogous to + The genes have diverged before a speciation event. + in between-species paralogy relationship with + + + + + + Paralogy that involves genes from different species. + + + - + - - - + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + post-displacement + in postdisplacement relationship with + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + - + - - - + + + + Peramorphosis that is produced by a delay in the offset of development. + + + in hypermorphosis relationship with + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + ISBN:978-0674639416 + - + - - - + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + synologous to + in synology relationship with + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + + - + - - - + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + ECO:0000080 + isoorthologous to + in isoorthology relationship with + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + - + - - - + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + tandem paralogous to + iterative paralogy + serial paralogy + in tandem paralogy relationship with + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + ISBN:978-0878932665 + - + - - - - - - true - - - + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + apomorphic tendency + cryptic homology + latent homologous to + underlying synapomorphy + homoiology + homoplastic tendency + re-awakening + Used for structures in closely related taxa. + in latent homology relationship with + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + + + ISBN:0199141118 + - + - - - + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + generative homology + syngenous to + Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + in syngeny relationship with + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R + - + - - - + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + 1:1 paralogy + apparent 1:1 orthology + apparent orthologous to + pseudoorthology + The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + in apparent orthology relationship with + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + + - + - - - + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + pseudoparalogous to + These genes may come out as paralogs in a single-genome analysis. + in pseudoparalogy relationship with + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + - + - - - - + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + equivalogous to + This may include examples of orthology, paralogy and xenology. + in equivalogy relationship with + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + - + - - - + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + interologous to + in interology relationship with + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + + - + - - - + + + + Similarity that is characterized by interchangeability in function. + + + functional similarity + in functional equivalence relationship with + + + + + + Similarity that is characterized by interchangeability in function. + + + + - + - - - + + + + Biological homology that involves parts of the same organism. + + + iterative homologous to + in iterative homology relationship with + + + + + + Biological homology that involves parts of the same organism. + + + - + - - - - + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + duplicate xenology + multiple xenology + paraxenologous to + in paraxenology relationship with + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + + - + - - - - + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + plerologous to + This phenomenon is usually due to gene conversion process. + in plerology relationship with + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + - + - - - + + + + + Structural homology that involves structures with the same or similar relative positions. + + + homotopous to + Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + in homotopy relationship with + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + + ISBN:0123195837 + - + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + heterotopy + in homeosis relationship with + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + + + + + + + + + + + + Synology that results from allopolyploidy. + + + homoeologous to + On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + in homoeology relationship with + + + + + + Synology that results from allopolyploidy. + + + + + + + + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + axis paramorphism + in paramorphism relationship with + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + + + + + + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + regulogous to + in regulogy relationship with + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + + + + + + + + + + + + + + + + + + + + + + + + 0 + + + 100 + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + dos + 2018-05-22T16:43:28Z + This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. + has increased age-specific mortality rate + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + PMID:24138933 + Wikipedia:Infant_mortality + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + spatial region + + + + + + + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + + disposition + + - + + + + - + + + + + + + + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + realizable entity + - + - - - - + + + + + + + + + quality + + + + + + + + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + + + + + + + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + generically dependent continuant + + + + + + + + + function + + + + + + + + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + + + + + + + immaterial entity + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + CARO:0000000 + Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure. + anatomical entity + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + CAROC:Brownsville2014 + + + + + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development. + connected anatomical structure + + + + + + + + + + + + + + + + An anatomical entity that has mass. + CARO:0000006 + material anatomical entity + + + + + + + + + + + + + + + + Anatomical entity that has no mass. + CARO:0000007 + immaterial anatomical entity + + + + + + + + + A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. + CARO:0001001 + neuron projection bundle + + + + + + + + + Material anatomical entity that is a member of an individual species or is a viral or viroid particle. + Melissa Haendel + organism or virus or viroid + + + + + + + + + An anatomical structure that has more than one cell as a part. + djs93 + CARO:0010000 + multicellular anatomical structure + + + + + + + + + + + + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CALOHA:TS-2035 + FBbt:00007002 + FMA:68646 + GO:0005623 + KUPO:0000002 + MESH:D002477 + VHOG:0001533 + WBbt:0004017 + XAO:0003012 + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + cell + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CARO:mah + + + + + + + + + Any neuron having a sensory function; an afferent neuron conveying sensory impulses. + BTO:0001037 + FBbt:00005124 + FMA:84649 + MESH:D011984 + WBbt:0005759 + sensory neuron + + + + + Any neuron having a sensory function; an afferent neuron conveying sensory impulses. + ISBN:0721662544 + + + + + + + + + + The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. + + BTO:0000938 + CALOHA:TS-0683 + FBbt:00005106 + FMA:54527 + VHOG:0001483 + WBbt:0003679 + nerve cell + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. + neuron + + + + + The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. + MESH:D009474 + http://en.wikipedia.org/wiki/Neuron + + + + + + + + + A system which has the disposition to environ one or more material entities. + 2013-09-23T16:04:08Z + EcoLexicon:environment + environment + In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. + environmental system + + + + + A system which has the disposition to environ one or more material entities. + DOI:10.1186/2041-1480-4-43 + + + + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + molecular function + GO:0003674 + Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. + molecular_function + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + GOC:pdt + + + + + + + + + + + + true + + + Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. + KEGG_REACTION:R03876 + Reactome:R-HSA-1169394 + Reactome:R-HSA-1169395 + Reactome:R-HSA-1169397 + Reactome:R-HSA-1169398 + Reactome:R-HSA-1169402 + Reactome:R-HSA-1169405 + Reactome:R-HSA-1169406 + Reactome:R-HSA-1234163 + Reactome:R-HSA-1234172 + Reactome:R-HSA-1253282 + Reactome:R-HSA-1358789 + Reactome:R-HSA-1358790 + Reactome:R-HSA-1358792 + Reactome:R-HSA-1363331 + Reactome:R-HSA-168915 + Reactome:R-HSA-173542 + Reactome:R-HSA-173545 + Reactome:R-HSA-174057 + Reactome:R-HSA-174104 + Reactome:R-HSA-174144 + Reactome:R-HSA-174159 + Reactome:R-HSA-174195 + Reactome:R-HSA-174227 + Reactome:R-HSA-179417 + Reactome:R-HSA-180540 + Reactome:R-HSA-180597 + Reactome:R-HSA-182986 + Reactome:R-HSA-182993 + Reactome:R-HSA-183036 + Reactome:R-HSA-183051 + Reactome:R-HSA-183084 + Reactome:R-HSA-183089 + Reactome:R-HSA-1852623 + Reactome:R-HSA-187575 + Reactome:R-HSA-1912357 + Reactome:R-HSA-1912386 + Reactome:R-HSA-1918092 + Reactome:R-HSA-1918095 + Reactome:R-HSA-1977296 + Reactome:R-HSA-1980074 + Reactome:R-HSA-1980118 + Reactome:R-HSA-201425 + Reactome:R-HSA-202453 + Reactome:R-HSA-202534 + Reactome:R-HSA-205118 + Reactome:R-HSA-209063 + Reactome:R-HSA-211734 + Reactome:R-HSA-2169050 + Reactome:R-HSA-2172172 + Reactome:R-HSA-2179276 + Reactome:R-HSA-2186747 + Reactome:R-HSA-2186785 + Reactome:R-HSA-2187368 + Reactome:R-HSA-2213017 + Reactome:R-HSA-264444 + Reactome:R-HSA-2682349 + Reactome:R-HSA-2730904 + Reactome:R-HSA-2737728 + Reactome:R-HSA-2769007 + Reactome:R-HSA-2900765 + Reactome:R-HSA-3000335 + Reactome:R-HSA-3134804 + Reactome:R-HSA-3134946 + Reactome:R-HSA-3249386 + Reactome:R-HSA-3780995 + Reactome:R-HSA-3781009 + Reactome:R-HSA-3788724 + Reactome:R-HSA-3797226 + Reactome:R-HSA-400267 + Reactome:R-HSA-4332236 + Reactome:R-HSA-446877 + Reactome:R-HSA-450358 + Reactome:R-HSA-451418 + Reactome:R-HSA-5205682 + Reactome:R-HSA-5357757 + Reactome:R-HSA-5362412 + Reactome:R-HSA-5483238 + Reactome:R-HSA-5607725 + Reactome:R-HSA-5607728 + Reactome:R-HSA-5607756 + Reactome:R-HSA-5607757 + Reactome:R-HSA-5610742 + Reactome:R-HSA-5610745 + Reactome:R-HSA-5610746 + Reactome:R-HSA-5652009 + Reactome:R-HSA-5655170 + Reactome:R-HSA-5660753 + Reactome:R-HSA-5667107 + Reactome:R-HSA-5667111 + Reactome:R-HSA-5668454 + Reactome:R-HSA-5668534 + Reactome:R-HSA-5675470 + Reactome:R-HSA-5684250 + Reactome:R-HSA-5691108 + Reactome:R-HSA-5693108 + Reactome:R-HSA-69598 + Reactome:R-HSA-741386 + Reactome:R-HSA-75824 + Reactome:R-HSA-870449 + Reactome:R-HSA-8948709 + Reactome:R-HSA-8956106 + Reactome:R-HSA-9013069 + Reactome:R-HSA-9013974 + Reactome:R-HSA-9014342 + Reactome:R-HSA-918224 + Reactome:R-HSA-936412 + Reactome:R-HSA-936942 + Reactome:R-HSA-936986 + Reactome:R-HSA-9628444 + Reactome:R-HSA-9645394 + Reactome:R-HSA-9645414 + Reactome:R-HSA-9688831 + Reactome:R-HSA-9701000 + Reactome:R-HSA-975118 + Reactome:R-HSA-975147 + Reactome:R-HSA-983140 + Reactome:R-HSA-983153 + Reactome:R-HSA-983156 + anaphase-promoting complex activity + ubiquitin conjugating enzyme activity + ubiquitin ligase activity + ubiquitin protein ligase activity + ubiquitin protein-ligase activity + ubiquitin-conjugating enzyme activity + E2 + E3 + GO:0004842 + ubiquitin-protein transferase activity + + + + + Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. + GOC:BioGRID + GOC:jh2 + PMID:9635407 + + + + + Reactome:R-HSA-1169394 + ISGylation of IRF3 + + + + + Reactome:R-HSA-1169395 + ISGylation of viral protein NS1 + + + + + Reactome:R-HSA-1169397 + Activation of ISG15 by UBA7 E1 ligase + + + + + Reactome:R-HSA-1169398 + ISGylation of host protein filamin B + + + + + Reactome:R-HSA-1169402 + ISGylation of E2 conjugating enzymes + + + + + Reactome:R-HSA-1169405 + ISGylation of protein phosphatase 1 beta (PP2CB) + + + + + Reactome:R-HSA-1169406 + ISGylation of host proteins + + + + + Reactome:R-HSA-1234163 + Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha + + + + + Reactome:R-HSA-1234172 + Nuclear VBC complex ubiquitinylates HIF-alpha + + + + + Reactome:R-HSA-1253282 + ERBB4 ubiquitination by WWP1/ITCH + + + + + Reactome:R-HSA-1358789 + Self-ubiquitination of RNF41 + + + + + Reactome:R-HSA-1358790 + RNF41 ubiquitinates ERBB3 + + + + + Reactome:R-HSA-1358792 + RNF41 ubiquitinates activated ERBB3 + + + + + Reactome:R-HSA-1363331 + Ubiquitination of p130 (RBL2) by SCF (Skp2) + + + + + Reactome:R-HSA-168915 + K63-linked ubiquitination of RIP1 bound to the activated TLR complex + + + + + Reactome:R-HSA-173542 + SMURF2 ubiquitinates SMAD2 + + + + + Reactome:R-HSA-173545 + Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling + + + + + Reactome:R-HSA-174057 + Multiubiquitination of APC/C-associated Cdh1 + + + + + Reactome:R-HSA-174104 + Ubiquitination of Cyclin A by APC/C:Cdc20 complex + + + + + Reactome:R-HSA-174144 + Ubiquitination of Securin by phospho-APC/C:Cdc20 complex + + + + + Reactome:R-HSA-174159 + Ubiquitination of Emi1 by SCF-beta-TrCP + + + + + Reactome:R-HSA-174195 + Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex + + + + + Reactome:R-HSA-174227 + Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex + + + + + Reactome:R-HSA-179417 + Multiubiquitination of Nek2A + + + + + Reactome:R-HSA-180540 + Multi-ubiquitination of APOBEC3G + + + + + Reactome:R-HSA-180597 + Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex + + + + + Reactome:R-HSA-182986 + CBL-mediated ubiquitination of CIN85 + + + + + Reactome:R-HSA-182993 + Ubiquitination of stimulated EGFR (CBL) + + + + + Reactome:R-HSA-183036 + Ubiquitination of stimulated EGFR (CBL:GRB2) + + + + + Reactome:R-HSA-183051 + CBL ubiquitinates Sprouty + + + + + Reactome:R-HSA-183084 + CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix + + + + + Reactome:R-HSA-183089 + CBL binds and ubiquitinates phosphorylated Sprouty + + + + + Reactome:R-HSA-1852623 + Ubiquitination of NICD1 by FBWX7 + + + + + Reactome:R-HSA-187575 + Ubiquitination of phospho-p27/p21 + + + + + Reactome:R-HSA-1912357 + ITCH ubiquitinates DTX + + + + + Reactome:R-HSA-1912386 + Ubiquitination of NOTCH1 by ITCH in the absence of ligand + + + + + Reactome:R-HSA-1918092 + CHIP (STUB1) mediates ubiquitination of ERBB2 + + + + + Reactome:R-HSA-1918095 + CUL5 mediates ubiquitination of ERBB2 + + + + + Reactome:R-HSA-1977296 + NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer + + + + + Reactome:R-HSA-1980074 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 + + + + + Reactome:R-HSA-1980118 + ARRB mediates NOTCH1 ubiquitination + + + + + Reactome:R-HSA-201425 + Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling + + + + + Reactome:R-HSA-202453 + Auto-ubiquitination of TRAF6 + + + + + Reactome:R-HSA-202534 + Ubiquitination of NEMO by TRAF6 + + + + + Reactome:R-HSA-205118 + TRAF6 polyubiquitinates NRIF + + + + + Reactome:R-HSA-209063 + Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex + + + + + Reactome:R-HSA-211734 + Ubiquitination of PAK-2p34 + + + + + Reactome:R-HSA-2169050 + SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7 + + + + + Reactome:R-HSA-2172172 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH2 + + + + + Reactome:R-HSA-2179276 + SMURF2 monoubiquitinates SMAD3 + + + + + Reactome:R-HSA-2186747 + Ubiquitination of SKI/SKIL by RNF111/SMURF2 + + + + + Reactome:R-HSA-2186785 + RNF111 ubiquitinates SMAD7 + + + + + Reactome:R-HSA-2187368 + STUB1 (CHIP) ubiquitinates SMAD3 + + + + + Reactome:R-HSA-2213017 + Auto-ubiquitination of TRAF3 + + + + + Reactome:R-HSA-264444 + Autoubiquitination of phospho-COP1(Ser-387 ) + + + + + Reactome:R-HSA-2682349 + RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels + + + + + Reactome:R-HSA-2730904 + Auto-ubiquitination of TRAF6 + + + + + Reactome:R-HSA-2737728 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants + + + + + Reactome:R-HSA-2769007 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants + + + + + Reactome:R-HSA-2900765 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants + + + + + Reactome:R-HSA-3000335 + SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA + + + + + Reactome:R-HSA-3134804 + STING ubiquitination by TRIM32 or TRIM56 + + + + + Reactome:R-HSA-3134946 + DDX41 ubiquitination by TRIM21 + + + + + Reactome:R-HSA-3249386 + DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1 + + + + + Reactome:R-HSA-3780995 + NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2 + + + + + Reactome:R-HSA-3781009 + NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1 + + + + + Reactome:R-HSA-3788724 + Cdh1:APC/C ubiquitinates EHMT1 and EHMT2 + + + + + Reactome:R-HSA-3797226 + Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease) + + + + + Reactome:R-HSA-400267 + BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins + + + + + Reactome:R-HSA-4332236 + CBL neddylates TGFBR2 + + + + + Reactome:R-HSA-446877 + TRAF6 is K63 poly-ubiquitinated + + + + + Reactome:R-HSA-450358 + Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation + + + + + Reactome:R-HSA-451418 + Pellino ubiquitinates IRAK1 + + + + + Reactome:R-HSA-5205682 + Parkin promotes the ubiquitination of mitochondrial substrates + + + + + Reactome:R-HSA-5357757 + BIRC(cIAP1/2) ubiquitinates RIPK1 + + + + + Reactome:R-HSA-5362412 + SYVN1 ubiquitinates Hh C-terminal fragments + + + + + Reactome:R-HSA-5483238 + Hh processing variants are ubiquitinated + + + + + Reactome:R-HSA-5607725 + SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP + + + + + Reactome:R-HSA-5607728 + beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex + + + + + Reactome:R-HSA-5607756 + TRAF6 oligomer autoubiquitinates + + + + + Reactome:R-HSA-5607757 + K63polyUb-TRAF6 ubiquitinates TAK1 + + + + + Reactome:R-HSA-5610742 + SCF(beta-TrCP) ubiquitinates p-GLI1 + + + + + Reactome:R-HSA-5610745 + SCF(beta-TrCP) ubiquitinates p-GLI2 + + + + + Reactome:R-HSA-5610746 + SCF(beta-TrCP) ubiquitinates p-GLI3 + + + + + Reactome:R-HSA-5652009 + RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA + + + + + Reactome:R-HSA-5655170 + RCHY1 monoubiquitinates POLH + + + + + Reactome:R-HSA-5660753 + SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA + + + + + Reactome:R-HSA-5667107 + SIAH1, SIAH2 ubiquitinate SNCAIP + + + + + Reactome:R-HSA-5667111 + PARK2 K63-Ubiquitinates SNCAIP + + + + + Reactome:R-HSA-5668454 + K63polyUb-cIAP1,2 ubiquitinates TRAF3 + + + + + Reactome:R-HSA-5668534 + cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK + + + + + Reactome:R-HSA-5675470 + BIRC2/3 (cIAP1/2) is autoubiquitinated + + + + + Reactome:R-HSA-5684250 + SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2 + + + + + Reactome:R-HSA-5691108 + SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2 + + + + + Reactome:R-HSA-5693108 + TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains + + + + + Reactome:R-HSA-69598 + Ubiquitination of phosphorylated Cdc25A + + + + + Reactome:R-HSA-741386 + RIP2 induces K63-linked ubiquitination of NEMO + + + + + Reactome:R-HSA-75824 + Ubiquitination of Cyclin D1 + + + + + Reactome:R-HSA-870449 + TRIM33 monoubiquitinates SMAD4 + + + + + Reactome:R-HSA-8948709 + DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3 + + + + + Reactome:R-HSA-8956106 + VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha + + + + + Reactome:R-HSA-9013069 + Ubiquitination of DLL/JAG ligands upon binding to NOTCH3 + + + + + Reactome:R-HSA-9013974 + Auto-ubiquitination of TRAF3 within activated TLR3 complex + + + + + Reactome:R-HSA-9014342 + K63-linked ubiquitination of RIP1 bound to the activated TLR complex + + + + + Reactome:R-HSA-918224 + DDX58 is K63 polyubiquitinated + + + + + Reactome:R-HSA-936412 + RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS + + + + + Reactome:R-HSA-936942 + Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 + + + + + Reactome:R-HSA-936986 + Activated TRAF6 synthesizes unanchored polyubiquitin chains + + + + + Reactome:R-HSA-9628444 + Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation + + + + + Reactome:R-HSA-9645394 + Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation + + + + + Reactome:R-HSA-9645414 + Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer + + + + + Reactome:R-HSA-9688831 + STUB1 ubiquitinates RIPK3 at K55, K363 + + + + + Reactome:R-HSA-9701000 + BRCA1:BARD1 heterodimer autoubiquitinates + + + + + Reactome:R-HSA-975118 + TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex + + + + + Reactome:R-HSA-975147 + Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane + + + + + Reactome:R-HSA-983140 + Transfer of Ub from E2 to substrate and release of E2 + + + + + Reactome:R-HSA-983153 + E1 mediated ubiquitin activation + + + + + Reactome:R-HSA-983156 + Polyubiquitination of substrate + + + + + anaphase-promoting complex activity + GOC:dph + GOC:tb + + + + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + NIF_Subcellular:sao1702920020 + Wikipedia:Cell_nucleus + cell nucleus + horsetail nucleus + GO:0005634 + nucleus + + + + + A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. + GOC:go_curators + + + + + horsetail nucleus + GOC:al + GOC:mah + GOC:vw + PMID:15030757 + + + + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + jl + 2012-09-19T15:05:24Z + Wikipedia:Biological_process + biological process + physiological process + single organism process + single-organism process + GO:0008150 + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. + biological_process + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + + + + + + true + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + Reactome:R-HSA-6788855 + Reactome:R-HSA-6788867 + phosphokinase activity + GO:0016301 + Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. + kinase activity + + + + + Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. + ISBN:0198506732 + + + + + Reactome:R-HSA-6788855 + FN3KRP phosphorylates PsiAm, RibAm + + + + + Reactome:R-HSA-6788867 + FN3K phosphorylates ketosamines + + + + + + + + + + + + true + + + Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. + Reactome:R-HSA-141367 + Reactome:R-HSA-162914 + GO:0019107 + myristoyltransferase activity + + + + + Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. + GOC:ai + + + + + Reactome:R-HSA-141367 + Myristoylation of tBID by NMT1 + + + + + Reactome:R-HSA-162914 + Myristoylation of Nef + - + - - - + + + A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. + disease + - + - - - + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATO:0000001 + quality + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + - - - + + + A branchiness quality inhering in a bearer by virtue of the bearer's having branches. + + ramified + ramiform + PATO:0000402 + branched + + + + + A branchiness quality inhering in a bearer by virtue of the bearer's having branches. + WordNet:WordNet + - - - - - - - - - + - - - - - - - - - + A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. + PATO:0001199 + linear + + + + + A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. + ISBN:0881923214 + - - - + + + A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. + + 2009-10-06T04:37:14Z + PATO:0002124 + laminar + + + + + A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. + PATOC:GVG + @@ -10207,7 +13669,6 @@ For example, protein A (transcription factor) indirectly increases by expression - @@ -10247,38 +13708,103 @@ For example, protein A (transcription factor) indirectly increases by expression - + A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 http://www.jbiomedsem.com/content/4/1/43 system - + - + - + phenotype + + + + + + + - + - - - - + - - - + + ## Elucidation + +This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + +## How to interpret (informal) + +First the &quot;atemporal&quot; FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + axiom holds for all times + + + + + + + + ## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y) + relation has no temporal argument + + + + @@ -10290,47 +13816,26 @@ For example, protein A (transcription factor) indirectly increases by expression /////////////////////////////////////////////////////////////////////////////////////// --> - - true - - - inverse of has disposition - - - - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. - - - - - - - - - - - - - + + + curation status specification - - + + + ready for release - - + + + pending final vetting - - + + + obsolescence reason specification - - is defined by + + + requires discussion - - - - is defined by - This is an experimental annotation - @@ -10392,6 +13897,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -10519,6 +14030,178 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z @@ -10709,7 +14392,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - diff --git a/src/metadata/README.md b/src/metadata/README.md new file mode 100644 index 00000000..4028d661 --- /dev/null +++ b/src/metadata/README.md @@ -0,0 +1,24 @@ +Metadata files for the OBO Library + + * [ro.yml](ro.yml) + * Determines how your purl.obolibrary.org/obo/ro/ redirects will be handled + * Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config + * Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config) + * Paste in the contents of [ro.yml](ro.yml) + * Click "Commit new file" + * IMPORTANT: remember to make a pull request + * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library* + * [ro.md](ro.md) + * Determines how your metadata is shown on OBO Library, OLS and AberOWL + * Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology + * Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology) + * Paste in the contents of [ro.md](ro.md) + * Click "Commit new file" + * IMPORTANT: remember to make a pull request + * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library* + +For more background see: + + * http://obofoundry.org/ + * http://obofoundry.org/faq/how-do-i-edit-metadata.html + diff --git a/src/metadata/ro.md b/src/metadata/ro.md new file mode 100644 index 00000000..2951a17a --- /dev/null +++ b/src/metadata/ro.md @@ -0,0 +1,44 @@ +--- +layout: ontology_detail +id: ro +title: OBO Relations Ontology +jobs: + - id: https://travis-ci.org/oborel/obo-relations + type: travis-ci +build: + checkout: git clone https://github.com/oborel/obo-relations.git + system: git + path: "." +contact: + email: + label: + github: +description: OBO Relations Ontology is an ontology... +domain: stuff +homepage: https://github.com/oborel/obo-relations +products: + - id: ro.owl + name: "OBO Relations Ontology main release in OWL format" + - id: ro.obo + name: "OBO Relations Ontology additional release in OBO format" + - id: ro.json + name: "OBO Relations Ontology additional release in OBOJSon format" + - id: ro/ro-base.owl + name: "OBO Relations Ontology main release in OWL format" + - id: ro/ro-base.obo + name: "OBO Relations Ontology additional release in OBO format" + - id: ro/ro-base.json + name: "OBO Relations Ontology additional release in OBOJSon format" +dependencies: +- id: omo + +tracker: https://github.com/oborel/obo-relations/issues +license: + url: http://creativecommons.org/licenses/by/3.0/ + label: CC-BY +activity_status: active +--- + +Enter a detailed description of your ontology here. You can use arbitrary markdown and HTML. +You can also embed images too. + diff --git a/src/metadata/ro.yml b/src/metadata/ro.yml new file mode 100644 index 00000000..2ea73243 --- /dev/null +++ b/src/metadata/ro.yml @@ -0,0 +1,27 @@ +# PURL configuration for http://purl.obolibrary.org/obo/ro + +idspace: RO +base_url: /obo/ro + +products: +- ro.owl: https://raw.githubusercontent.com/oborel/obo-relations/main/ro.owl +- ro.obo: https://raw.githubusercontent.com/oborel/obo-relations/main/ro.obo + +term_browser: ontobee +example_terms: +- RO_0000000 + +entries: + +- prefix: /releases/ + replacement: https://raw.githubusercontent.com/oborel/obo-relations/v + +- prefix: /tracker/ + replacement: https://github.com/oborel/obo-relations/issues + +- prefix: /about/ + replacement: http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/ + +## generic fall-through, serve direct from github by default +- prefix: / + replacement: https://raw.githubusercontent.com/oborel/obo-relations/main/ diff --git a/src/ontology/Makefile b/src/ontology/Makefile index eaf2551b..9363f5d8 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,229 +1,745 @@ -OBO=http://purl.obolibrary.org/obo -ONT=ro -ONTBASE=$(OBO)/$(ONT) +# ---------------------------------------- +# Makefile for ro +# Generated using ontology-development-kit +# ODK Version: v1.4 +# ---------------------------------------- +# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use ro.Makefile instead -SRC=ro-edit.owl -CATALOG=catalog-v001.xml -ROBOT=robot --catalog $(CATALOG) -REPORT_FAIL_ON = ERROR -RELEASEDATE ?= `date +%Y-%m-%d` -ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(RELEASEDATE)/$@ --annotation owl:versionInfo $(RELEASEDATE) +# ---------------------------------------- +# More information: https://github.com/INCATools/ontology-development-kit/ -ONTS_TO_BUILD= ro.obo ro.owl ro.json ro-base.owl ro-base.obo ro-base.json chemical.owl annotations.owl other_import.owl core.owl go-biotic.owl pato_import.owl temporal-intervals.owl bfo-axioms.owl bfo-classes-minimal.owl el-constraints.owl go_mf_import.owl go_cc_import.owl generated-axioms.owl omo_import.owl -ONTS= $(ONTS_TO_BUILD) rohom.owl -# ======================================== -# PRODUCTION -# ======================================== +# ---------------------------------------- +# Standard Constants +# ---------------------------------------- +# these can be overwritten on the command line + +OBOBASE= http://purl.obolibrary.org/obo +URIBASE= http://purl.obolibrary.org/obo +ONT= ro +ONTBASE= http://purl.obolibrary.org/obo/ro +EDIT_FORMAT= owl +SRC = $(ONT)-edit.$(EDIT_FORMAT) +MAKE_FAST= $(MAKE) IMP=false PAT=false COMP=false MIR=false +CATALOG= catalog-v001.xml +ROBOT= robot --catalog $(CATALOG) + +OWLTOOLS= owltools --use-catalog +RELEASEDIR= ../.. +REPORTDIR= reports +TEMPLATEDIR= ../templates +TMPDIR= tmp +MIRRORDIR= mirror +IMPORTDIR= imports +SUBSETDIR= subsets +SCRIPTSDIR= ../scripts +UPDATEREPODIR= target +SPARQLDIR = ../sparql +COMPONENTSDIR = components +ROBOT_PROFILE = profile.txt +REPORT_FAIL_ON = ERROR +REPORT_LABEL = +REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE) +OBO_FORMAT_OPTIONS = +SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by +SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms +ODK_VERSION_MAKEFILE = v1.4 + +TODAY ?= $(shell date +%Y-%m-%d) +OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') +VERSION= $(TODAY) +ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION) +ANNOTATE_CONVERT_FILE = annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@ +OTHER_SRC = $(COMPONENTSDIR)/core.owl $(COMPONENTSDIR)/el-constraints.owl $(COMPONENTSDIR)/generated-axioms.owl $(COMPONENTSDIR)/temporal-intervals.owl $(COMPONENTSDIR)/bfo-axioms.owl $(COMPONENTSDIR)/bfo-classes-minimal.owl $(COMPONENTSDIR)/rohom.owl +ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt +EDIT_PREPROCESSED = $(TMPDIR)/$(ONT)-preprocess.owl + +FORMATS = $(sort owl obo json owl) +FORMATS_INCL_TSV = $(sort $(FORMATS) tsv) +RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full core ) -all: build +# ---------------------------------------- +# Top-level targets +# ---------------------------------------- + +.PHONY: .FORCE + +.PHONY: all +all: all_odk -test: - robot reason -r HermiT -i ro-edit.owl +.PHONY: all_odk +all_odk: odkversion test all_assets -build: ro.owl ro.obo ro.json all_subsets +.PHONY: test +test: odkversion reason_test sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt + echo "Finished running all tests successfully." -release: all $(ONTS_TO_BUILD) - cp -pr catalog-v001.xml $(ONTS) subsets ../.. +.PHONY: release_diff +release_diff: $(REPORTDIR)/release-diff.md -# fairly dump release process whilst waiting for Oort - check than versionIRI has been entered manually. -ro.owl: ro-edit.owl core.owl temporal-intervals.owl validate-using-oort - $(ROBOT) reason -i $< --axiom-generators "SubClass SubObjectProperty ObjectPropertyRange ObjectPropertyDomain" \ - annotate --ontology-iri $(OBO)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@ +.PHONY: reason_test +reason_test: $(EDIT_PREPROCESSED) + $(ROBOT) reason --input $< --reasoner ELK --equivalent-classes-allowed asserted-only \ + --exclude-tautologies structural --output test.owl && rm test.owl -# grep versionIRI $< && (echo "check the version:" && echo versionIRI: `grep versionIRI $<` && cp $< $@) || echo 'You must set the versionIRI!!' +.PHONY: odkversion +odkversion: + echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, \ + not the version of the ODK you are running)" &&\ + echo "ROBOT version (ODK): " && $(ROBOT) --version -# turtle file is merged, for querying via arq -ro.ttl: ro.owl - owltools --use-catalog $< --merge-import-closure -o -f ttl $@.tmp && mv $@.tmp $@ +$(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR): + mkdir -p $@ + +# ---------------------------------------- +# Release assets +# ---------------------------------------- -EXT_IMPORTS = pato_import go_cc_import go_mf_import go-biotic other_import annotations +MAIN_PRODUCTS = $(sort $(foreach r,$(RELEASE_ARTEFACTS), $(r)) $(ONT)) +MAIN_GZIPPED = +MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) $(MAIN_GZIPPED) +SRCMERGED = $(TMPDIR)/merged-$(SRC) -ro-base.owl: ro-edit.owl - owltools --use-catalog $< $(patsubst %, --remove-import-declaration $(OBO)/ro/%.owl, $(EXT_IMPORTS)) --merge-imports-closure --set-ontology-id -v $(OBO)/ro/releases/$(RELEASEDATE)/$@ $(OBO)/ro/$@ -o $@ +.PHONY: all_main +all_main: $(MAIN_FILES) -%.obo: %.owl - owltools --use-catalog $< --merge-import-closure -o -f obo $@.tmp && mv $@.tmp $@ +# ---------------------------------------- +# Import assets +# ---------------------------------------- -%.json: %.owl - owltools --use-catalog $< --merge-import-closure -o -f json $@.tmp && mv $@.tmp $@ -%-sh.obo: %.owl - owltools --use-catalog $< --merge-import-closure --add-obo-shorthand-to-properties -o -f obo $@.tmp && grep -v ^owl-axioms $@.tmp > $@ +IMPORTS = omo pato cl envo go caro other -# soon this will be incorporated into Oort -ro-el.owl: ro.owl - makeElWithoutReasoning.sh -i `pwd`/$< -o `pwd`/$@ +IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) +IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) +IMPORT_FILES = $(IMPORT_OWL_FILES) -# note we don't do anything with the generated ontology, this is just for checking purposes. -validate-using-oort: ro-edit.owl - ontology-release-runner --catalog-xml catalog-v001.xml --outdir build --simple --allow-overwrite --reasoner hermit ro-edit.owl - touch $@ -# ======================================== -# DOCUMENTATION -# ======================================== -# requires mkdocs: `pip install mkdocs` -docs-serve: - (cd ../.. && mkdocs serve) -docs-deploy: - (cd ../.. && mkdocs gh-deploy) - - -# ======================================== -# DIFFS -# ======================================== -ro-lastbuild.owl: ro-edit.owl - wget --no-check-certificate $(OBO)/ro.owl -O $@ - -ro-diff.md: ro.owl ro-lastbuild.owl - $(ROBOT) diff --left ro-lastbuild.owl --right $< -f markdown -o $@ -ro-diff.html: ro-diff.md - pandoc $< -o $@ - -# ======================================== -# IMPORTS -# ======================================== -seed.txt: $(SRC) - $(ROBOT) query -f csv -i $< --query sparql/terms.sparql $@ - -imports/%_terms_combined.txt: seed.txt - cat $< imports/$*_terms.txt | sort | uniq > $@ - -%_import.owl: mirror/%.owl imports/%_terms.txt - $(ROBOT) extract -i $< -T imports/$*_terms.txt --method BOT -O $(BASE)/$@ -o $@ -.PRECIOUS: imports/%_import.owl - -mirror/%.owl: - wget --no-check-certificate $(OBO)/$*.owl -O $@ - -# ======================================== -# MIREOT -# ======================================== - -bfo2-classes.owl: - owltools $(OBO)/bfo.owl --make-subset-by-properties // --set-ontology-id $(OBO)/ro/bfo2-classes.owl -o file://`pwd`/bfo2-classes.owl - -# ======================================== -# SUBSETS -# ======================================== -SUBSETS = interaction sequence time-interval mereotopology causal developmental eco hom -all_subsets: all_subsets_owl all_subsets_obo -all_subsets_owl: $(patsubst %,subsets/ro-%.owl,$(SUBSETS)) -all_subsets_obo: $(patsubst %,subsets/ro-%.obo,$(SUBSETS)) subsets/ro-chado.obo - -# generated by oort: -subsets/ro-eco.owl: build/subsets/ro-eco.owl - owltools --use-catalog $< --remove-dangling -o $@ - - -subsets/ro-biotic-interaction.owl: ro.owl - robot filter -i $< --term RO:0002437 --select "annotations self descendants" -o $@.tmp.owl && mv $@.tmp.owl $@ - -# the following subsets are generated purely by hierarchy: -subsets/ro-interaction.owl: ro.owl - owltools --use-catalog $< --extract-properties -s --list 'interacts with' // --set-ontology-id $(OBO)/ro/$@ -o $@ -subsets/ro-sequence.owl: ro.owl - owltools --use-catalog $< --extract-properties -s --list 'sequentially related to' // --set-ontology-id $(OBO)/ro/$@ -o $@ -subsets/ro-time-interval.owl: ro.owl - owltools --use-catalog $< --extract-properties -s --list 'temporally related to' // --set-ontology-id $(OBO)/ro/$@ -o $@ -subsets/ro-mereotopology.owl: ro.owl - owltools --use-catalog $< --extract-properties -s --list 'mereotopologically related to' // --set-ontology-id $(OBO)/ro/$@ -o $@ -subsets/ro-causal.owl: ro.owl - owltools --use-catalog $< --extract-properties -s --list 'causally related to' // --set-ontology-id $(OBO)/ro/$@ -o $@ -subsets/ro-developmental.owl: ro.owl - owltools --use-catalog $< --extract-properties -s --list 'developmentally related to' // --set-ontology-id $(OBO)/ro/$@ -o $@ -#subsets/ro-eco.owl: ro.owl -# owltools --use-catalog $< --extract-properties -s --list 'ecologically related to' // --set-ontology-id $(OBO)/ro/$@ -o $@ -subsets/ro-hom.owl: ro.owl - owltools --use-catalog $< --extract-properties -s --list 'in similarity relationship with' // --set-ontology-id $(OBO)/ro/$@ -o $@ - -subsets/%.csv: subsets/%.owl - robot query -i $< -s sparql/objectProperties.sparql $@.tmp -f csv && mv $@.tmp $@ - - -subsets/ro-chado.obo: ro.obo - owltools --use-catalog $< --merge-imports-closure --remove-tbox --remove-annotation-assertions -r -l -s -d --remove-dangling --set-ontology-id $(OBO)/ro/$@ -o -f obo $@.tmp && ../tools/translate-to-chado-obo.pl $@.tmp > $@ - -# ======================================== -# REPORTING (EXPERIMENTAL) -# ======================================== -# requires sparqlprog - -usage.tsv: ro-base.owl - pq-ontobee -f tsv -e -i $< "owl:objectProperty(P), label(P,PN), (ontobee ?? aggregate_group(count(Restr),[P,G],rdf(Restr,owl:onProperty,P,G),Num))" "x(P,PN,G,Num)" > $@.tmp && mv $@.tmp $@ -usage-full.tsv: - pq-ontobee -f tsv -e -i ro.owl "owl:objectProperty(P), (ontobee ?? rdf(Restr,owl:onProperty,P,G),label(P,PN))" "x(Restr,P,PN,G)" > $@.tmp && mv $@.tmp $@ - -# ======================================== -# EXPERIMENTAL -# ======================================== - -# Oort requires more testing before it can be used for a relations ontology. -# for now, just go with a simple release process (see above) -build-using-oort: ro-edit.owl - ontology-release-runner --catalog-xml catalog-v001.xml --outdir build --simple --allow-overwrite --reasoner hermit ro-edit.owl - touch $@ +.PHONY: all_imports +all_imports: $(IMPORT_FILES) -hom.obo: - wget $(OBO)/hom.obo -O $@.tmp && mv $@.tmp $@ -hom-fixed.obo: hom.obo - obo-grep.pl --neg -r is_obsolete: $< > $@.tmp && mv $@.tmp $@ +# ---------------------------------------- +# Subset assets +# ---------------------------------------- -rohom.obo: hom-fixed.obo - ../tools/hom2rhom.pl $< > $@.tmp && mv $@.tmp $@ -rohom.owl: rohom.obo - owltools $< -o $@.tmp && grep -v 'oboInOwl:id' $@.tmp > $@.tmp2 && $(HOME)/repos/uberon/util/expand-dbxref-literals.pl $@.tmp2 > $@ -## ODPs +SUBSETS = ro-interaction ro-sequence ro-time-interval ro-mereotopology ro-causal ro-developmental ro-eco ro-hom ro-chado ro-biotic-interaction -odp/%.owl: - wget http://www.ontologydesignpatterns.org/cp/owl/$*.owl -O $@ +SUBSET_ROOTS = $(patsubst %, $(SUBSETDIR)/%, $(SUBSETS)) +SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f))) +.PHONY: all_subsets +all_subsets: $(SUBSET_FILES) # ---------------------------------------- -# Reports +# Mapping assets # ---------------------------------------- -REPORTS=basicReport -all_reports: $(patsubst %, reports/envo-%.csv, $(REPORTS)) reports/ro.owl-obo-report.tsv -reports/ro-%.csv: sparql/%.sparql ro.owl - robot query -i ro.owl -s $< $@.tmp -f csv && mv $@.tmp $@ -# SPARQL constructs -reports/ro-%.ttl: sparql/%.sparql ro.owl - robot query -i ro.owl -c $< $@.tmp.ttl -f ttl && robot annotate -i $@.tmp.ttl -O $(OBO)/ro/$@ -o $@ +MAPPINGS = + +MAPPING_FILES = $(patsubst %, $(MAPPINGDIR)/%.sssom.tsv, $(MAPPINGS)) + +.PHONY: all_mappings +all_mappings: $(MAPPING_FILES) -views/%.owl: sparql/%.sparql ro.owl - robot merge -i ro.owl query -c $< $@.tmp.ttl -f ttl && robot annotate -i $@.tmp.ttl -O $(OBO)/ro/$@ -o $@ -gen-%.owl: sparql/construct-%.sparql ro.owl - robot query -i ro.owl -c $< $@.tmp.ttl -f ttl && robot annotate -i $@.tmp.ttl -O $(OBO)/ro/$@ -o $@ +# ---------------------------------------- +# QC Reports & Utilities +# ---------------------------------------- -# See https://github.com/oborel/obo-relations/pull/270 -GENAXIOMS = gen-universal-from-homeomorphy.owl -generated-axioms.owl: $(GENAXIOMS) - robot merge $(patsubst %, -i %, $(GENAXIOMS)) -o $@.tmp.ttl && robot annotate -i $@.tmp.ttl -O $(OBO)/ro/$@ -o $@ +OBO_REPORT = $(SRC)-obo-report +REPORTS = $(OBO_REPORT) +REPORT_FILES = $(patsubst %, $(REPORTDIR)/%.tsv, $(REPORTS)) -# generate includes from sparql CONSTRUCT queries; -# these can then be merged in to the main ontology -#reports/include-%.owl: sparql/construct-%.sparql ecto-core.owl +.PHONY: robot_reports +robot_reports: $(REPORT_FILES) + +.PHONY: all_reports +all_reports: custom_reports robot_reports + +# ---------------------------------------- +# ROBOT OWL Profile checking +# ---------------------------------------- + +# The merge step is necessary to avoid undeclared entity violations. +$(REPORTDIR)/validate_profile_owl2dl_%.txt: % | $(REPORTDIR) $(TMPDIR) + $(ROBOT) merge -i $< convert -f ofn -o $(TMPDIR)/validate.ofn + $(ROBOT) validate-profile --profile DL -i $(TMPDIR)/validate.ofn -o $@ || { cat $@ && exit 1; } +.PRECIOUS: $(REPORTDIR)/validate_profile_owl2dl_%.txt + +validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt + echo "$* profile validation completed." + +# ---------------------------------------- +# Sparql queries: Q/C +# ---------------------------------------- + +# these live in the ../sparql directory, and have suffix -violation.sparql +# adding the name here will make the violation check live. + +SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql) + +sparql_test: $(EDIT_PREPROCESSED) catalog-v001.xml | $(REPORTDIR) +ifneq ($(SPARQL_VALIDATION_QUERIES),) + + $(ROBOT) verify --catalog catalog-v001.xml -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) +endif # ---------------------------------------- # ROBOT report # ---------------------------------------- -reports/%-obo-report.tsv: % - $(ROBOT) merge --collapse-import-closure true -i $< report --labels true --fail-on $(REPORT_FAIL_ON) --print 5 -o $@ + +$(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR) + $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri http://purl.obolibrary.org/obo/RO_ --base-iri http://purl.obolibrary.org/obo/BFO_0000050 --base-iri http://purl.obolibrary.org/obo/BFO_0000051 --base-iri http://purl.obolibrary.org/obo/BFO_0000060 --print 5 -o $@ + +$(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR) + $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri http://purl.obolibrary.org/obo/RO_ --base-iri http://purl.obolibrary.org/obo/BFO_0000050 --base-iri http://purl.obolibrary.org/obo/BFO_0000051 --base-iri http://purl.obolibrary.org/obo/BFO_0000060 --print 5 -o $@ # ---------------------------------------- -# MARKDOWN EXPORT +# Release assets # ---------------------------------------- -markdown: ro.owl - owltools $< --merge-imports-closure --ontology-to-markdown -l 0 md + +ASSETS = \ + $(IMPORT_FILES) \ + $(MAIN_FILES) \ + $(REPORT_FILES) \ + $(SUBSET_FILES) \ + $(MAPPING_FILES) + +RELEASE_ASSETS = \ + $(MAIN_FILES) \ + $(SUBSET_FILES) + +.PHONY: all_assets +all_assets: $(ASSETS) + +.PHONY: show_assets +show_assets: + echo $(ASSETS) + du -sh $(ASSETS) + +check_rdfxml_%: % + @check-rdfxml $< + +.PHONY: check_rdfxml_assets +check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl) + +# ---------------------------------------- +# Release Management +# ---------------------------------------- + +CLEANFILES=$(MAIN_FILES) $(SRCMERGED) $(EDIT_PREPROCESSED) +# This should be executed by the release manager whenever time comes to make a release. +# It will ensure that all assets/files are fresh, and will copy to release folder + +.PHONY: prepare_release +prepare_release: all_odk + rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\ + rm -f $(CLEANFILES) &&\ + echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release \ + on your git hosting site such as GitHub or GitLab" + +.PHONY: prepare_initial_release +prepare_initial_release: all_assets + rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\ + rm -f $(patsubst %, ./%, $(CLEANFILES)) &&\ + cd $(RELEASEDIR) && git add $(RELEASE_ASSETS) + +.PHONY: prepare_release_fast +prepare_release_fast: + $(MAKE) prepare_release IMP=false PAT=false MIR=false COMP=false + +CURRENT_RELEASE=$(ONTBASE).owl + +$(TMPDIR)/current-release.owl: + wget $(CURRENT_RELEASE) -O $@ + +$(REPORTDIR)/release-diff.md: $(ONT).owl $(TMPDIR)/current-release.owl + $(ROBOT) diff --labels true --left $(TMPDIR)/current-release.owl --right $(ONT).owl -f markdown -o $@ + +# ------------------------ +# Imports: Seeding system +# ------------------------ + +# seed.txt contains all referenced entities +IMPORTSEED=$(TMPDIR)/seed.txt +PRESEED=$(TMPDIR)/pre_seed.txt + +$(SRCMERGED): $(EDIT_PREPROCESSED) $(OTHER_SRC) + $(ROBOT) remove --input $< --select imports --trim false \ + merge $(patsubst %, -i %, $(OTHER_SRC)) -o $@ + +$(EDIT_PREPROCESSED): $(SRC) + $(ROBOT) convert --input $< --format ofn --output $@ + +$(PRESEED): $(SRCMERGED) + $(ROBOT) query -f csv -i $< --query ../sparql/terms.sparql $@.tmp &&\ + cat $@.tmp | sort | uniq > $@ + + + +ALLSEED = $(PRESEED) \ + + +$(IMPORTSEED): $(ALLSEED) | $(TMPDIR) + if [ $(IMP) = true ]; then cat $(ALLSEED) | sort | uniq > $@; fi + +ANNOTATION_PROPERTIES=rdfs:label IAO:0000115 + +# ---------------------------------------- +# Import modules +# ---------------------------------------- +# Most ontologies are modularly constructed using portions of other ontologies +# These live in the imports/ folder +# This pattern uses ROBOT to generate an import module + +# Should be able to drop this if robot can just take a big messy list of terms as input. +$(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt + if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi + + + + +$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ + $(ANNOTATE_CONVERT_FILE); fi + +.PRECIOUS: $(IMPORTDIR)/%_import.owl + +## Module for ontology: omo + +$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/omo_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ + remove --base-iri $(OBOBASE)/OMO --axioms external --preserve-structure false --trim false \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/omo_terms_combined.txt --select complement \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ + $(ANNOTATE_CONVERT_FILE); fi + +## Module for ontology: pato + +$(IMPORTDIR)/pato_import.owl: $(MIRRORDIR)/pato.owl $(IMPORTDIR)/pato_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/pato_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ + remove --base-iri $(URIBASE)/PATO --axioms external --preserve-structure false --trim false \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/pato_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + $(ANNOTATE_CONVERT_FILE); fi + +## Module for ontology: cl + +$(IMPORTDIR)/cl_import.owl: $(MIRRORDIR)/cl.owl $(IMPORTDIR)/cl_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/cl_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ + remove --base-iri $(URIBASE)/CL --axioms external --preserve-structure false --trim false \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/cl_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + $(ANNOTATE_CONVERT_FILE); fi + +## Module for ontology: envo + +$(IMPORTDIR)/envo_import.owl: $(MIRRORDIR)/envo.owl $(IMPORTDIR)/envo_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/envo_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ + remove --base-iri $(URIBASE)/ENVO --axioms external --preserve-structure false --trim false \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/envo_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + $(ANNOTATE_CONVERT_FILE); fi + +## Module for ontology: go + +$(IMPORTDIR)/go_import.owl: $(MIRRORDIR)/go.owl $(IMPORTDIR)/go_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/go_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ + remove --base-iri $(URIBASE)/GO --axioms external --preserve-structure false --trim false \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/go_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + $(ANNOTATE_CONVERT_FILE); fi + +## Module for ontology: caro + +$(IMPORTDIR)/caro_import.owl: $(MIRRORDIR)/caro.owl $(IMPORTDIR)/caro_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/caro_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ + remove --base-iri $(URIBASE)/CARO --axioms external --preserve-structure false --trim false \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/caro_terms_combined.txt --select complement --select "classes individuals annotation-properties" \ + $(ANNOTATE_CONVERT_FILE); fi + +## Module for ontology: other + +$(IMPORTDIR)/other_import.owl: + echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in ro.Makefile!" && false + +.PHONY: refresh-imports +refresh-imports: + $(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B + +.PHONY: no-mirror-refresh-imports +no-mirror-refresh-imports: + $(MAKE) IMP=true MIR=false PAT=false IMP_LARGE=true all_imports -B + +.PHONY: refresh-imports-excluding-large +refresh-imports-excluding-large: + $(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=false all_imports -B + +.PHONY: refresh-% +refresh-%: + $(MAKE) IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl -B + +.PHONY: no-mirror-refresh-% +no-mirror-refresh-%: + $(MAKE) IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B + + +# ---------------------------------------- +# Components +# ---------------------------------------- +# Some ontologies contain external and internal components. A component is included in the ontology in its entirety. + +COMP=true # Global parameter to bypass component generation + +.PHONY: all_components +all_components: $(OTHER_SRC) + +.PHONY: recreate-components +recreate-components: + $(MAKE) COMP=true IMP=false MIR=true PAT=true IMP_LARGE=false all_components -B + +.PHONY: no-mirror-recreate-components +no-mirror-recreate-components: + $(MAKE) COMP=true IMP=false MIR=false PAT=true IMP_LARGE=false all_components -B + +.PHONY: recreate-% +recreate-%: + $(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=true PAT=true $(COMPONENTSDIR)/$*.owl -B + +.PHONY: no-mirror-recreate-% +no-mirror-recreate-%: + $(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl -B + +$(COMPONENTSDIR)/%: | $(COMPONENTSDIR) + touch $@ +.PRECIOUS: $(COMPONENTSDIR)/% + + + + + + + + +# ---------------------------------------- +# Mirroring upstream ontologies +# ---------------------------------------- + +IMP=true # Global parameter to bypass import generation +MIR=true # Global parameter to bypass mirror generation +IMP_LARGE=true # Global parameter to bypass handling of large imports + + + +## ONTOLOGY: omo +.PHONY: mirror-omo +.PRECIOUS: $(MIRRORDIR)/omo.owl +mirror-omo: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + + +## ONTOLOGY: pato +.PHONY: mirror-pato +.PRECIOUS: $(MIRRORDIR)/pato.owl +mirror-pato: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pato.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl && \ + $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PATO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + + +## ONTOLOGY: cl +.PHONY: mirror-cl +.PRECIOUS: $(MIRRORDIR)/cl.owl +mirror-cl: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cl.owl --create-dirs -o $(MIRRORDIR)/cl.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/cl.owl -o $@.tmp.owl && \ + $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CL --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + + +## ONTOLOGY: envo +.PHONY: mirror-envo +.PRECIOUS: $(MIRRORDIR)/envo.owl +mirror-envo: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/envo.owl --create-dirs -o $(MIRRORDIR)/envo.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/envo.owl -o $@.tmp.owl && \ + $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/ENVO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + + +## ONTOLOGY: go +.PHONY: mirror-go +.PRECIOUS: $(MIRRORDIR)/go.owl +mirror-go: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/go.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl && \ + $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/GO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + + +## ONTOLOGY: caro +.PHONY: mirror-caro +.PRECIOUS: $(MIRRORDIR)/caro.owl +mirror-caro: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/caro.owl --create-dirs -o $(MIRRORDIR)/caro.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o $@.tmp.owl && \ + $(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CARO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + + +## ONTOLOGY: other +## You have configured your default mirror type to no_mirror. + + +$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) + if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ + cp $(TMPDIR)/mirror-$*.owl $@; fi; fi + + + + +# ---------------------------------------- +# Subsets +# ---------------------------------------- +$(SUBSETDIR)/%.tsv: $(SUBSETDIR)/%.owl + $(ROBOT) query -f tsv -i $< -s ../sparql/labels.sparql $@ +.PRECIOUS: $(SUBSETDIR)/%.tsv + +$(SUBSETDIR)/%.owl: $(ONT).owl | $(SUBSETDIR) + $(OWLTOOLS) $< --extract-ontology-subset --fill-gaps --subset $* -o $@.tmp.owl && mv $@.tmp.owl $@ &&\ + $(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@.tmp.owl && mv $@.tmp.owl $@ +.PRECIOUS: $(SUBSETDIR)/%.owl + + +$(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo + +$(SUBSETDIR)/%.json: $(SUBSETDIR)/%.owl + $(ROBOT) convert --input $< --check false -f json -o $@.tmp.json &&\ + mv $@.tmp.json $@ + + +# --------------------------------------------- +# Sparql queries: Table exports / Query Reports +# --------------------------------------------- + +SPARQL_EXPORTS_ARGS = $(foreach V,$(SPARQL_EXPORTS),-s $(SPARQLDIR)/$(V).sparql $(REPORTDIR)/$(V).tsv) +# This combines all into one single command + +.PHONY: custom_reports +custom_reports: $(EDIT_PREPROCESSED) | $(REPORTDIR) +ifneq ($(SPARQL_EXPORTS_ARGS),) + $(ROBOT) query -f tsv --use-graphs true -i $< $(SPARQL_EXPORTS_ARGS) +endif + +# ---------------------------------------- +# Release artefacts: export formats +# ---------------------------------------- + + +$(ONT)-base.obo: $(ONT)-base.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +$(ONT)-base.json: $(ONT)-base.owl + $(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + convert --check false -f json -o $@.tmp.json &&\ + mv $@.tmp.json $@ +$(ONT)-full.obo: $(ONT)-full.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +$(ONT)-full.json: $(ONT)-full.owl + $(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + convert --check false -f json -o $@.tmp.json &&\ + mv $@.tmp.json $@ +core.obo: core.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +core.json: core.owl + $(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + convert --check false -f json -o $@.tmp.json &&\ + mv $@.tmp.json $@ +# ---------------------------------------- +# Release artefacts: main release artefacts +# ---------------------------------------- + +$(ONT).owl: $(ONT)-full.owl + $(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + convert -o $@.tmp.owl && mv $@.tmp.owl $@ + +$(ONT).obo: $(ONT).owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +$(ONT).json: $(ONT).owl + $(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + convert --check false -f json -o $@.tmp.json &&\ + mv $@.tmp.json $@ +# ----------------------------------------------------- +# Release artefacts: variants (base, full, simple, etc) +# ----------------------------------------------------- +SHARED_ROBOT_COMMANDS = + +$(ONTOLOGYTERMS): $(SRCMERGED) + $(ROBOT) query -f csv -i $< --query ../sparql/ro_terms.sparql $@ + +# ROBOT pipeline that merges imports, including components. +ROBOT_RELEASE_IMPORT_MODE=$(ROBOT) merge --input $< + +# ROBOT pipeline that removes imports, then merges components. This is for release artefacts that start from "base" +ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --trim false merge $(patsubst %, -i %, $(OTHER_SRC)) + +# base: All the axioms as they are editted by the editors, excluding reasoning +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) + $(ROBOT_RELEASE_IMPORT_MODE_BASE) \ + $(SHARED_ROBOT_COMMANDS) \ + annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ + --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + --output $@.tmp.owl && mv $@.tmp.owl $@ +# Full: The full artefacts with imports merged, reasoned. +$(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \ + relax \ + reduce -r ELK \ + $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ + +core.owl: + echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in ro.Makefile!" && false +# ---------------------------------------- +# Debugging Tools +# ---------------------------------------- + +explain_unsat: $(EDIT_PREPROCESSED) + $(ROBOT) explain -i $< -M unsatisfiability --unsatisfiable random:10 --explanation $(TMPDIR)/$@.md + + + +RELEASE_ASSETS_AFTER_RELEASE=$(foreach n,$(RELEASE_ASSETS), ../../$(n)) +GHVERSION=v$(VERSION) + +.PHONY: public_release +public_release: + @test $(GHVERSION) + ls -alt $(RELEASE_ASSETS_AFTER_RELEASE) + gh release create $(GHVERSION) --title "$(VERSION) Release" --draft $(RELEASE_ASSETS_AFTER_RELEASE) --generate-notes + +# ---------------------------------------- +# General Validation +# ---------------------------------------- +TSV= +ALL_TSV_FILES= + +validate-tsv: $(TSV) | $(TMPDIR) + for FILE in $< ; do \ + tsvalid $$FILE > $(TMPDIR)/validate.txt; \ + if [ -s $(TMPDIR)/validate.txt ]; then cat $(TMPDIR)/validate.txt && exit 1; fi ; \ + done + +validate-all-tsv: $(ALL_TSV_FILES) + $(MAKE) validate-tsv TSV="$^" + +# ---------------------------------------- +# Editors Utilities +# ---------------------------------------- + -merge_template: ../templates/new_relations.tsv - $(ROBOT) template --merge-before --input $(SRC) \ - --template $< --output $(SRC).ofn && mv $(SRC).ofn $(SRC) - \ No newline at end of file +.PHONY: normalize_src +normalize_src: $(SRC) + $(ROBOT) convert -i $< -f ofn -o $(TMPDIR)/normalise && mv $(TMPDIR)/normalise $< + +.PHONY: validate_idranges +validate_idranges: + amm $(SCRIPTSDIR)/validate_id_ranges.sc ro-idranges.owl + +.PHONY: update_repo +update_repo: + sh $(SCRIPTSDIR)/update_repo.sh + + + +# Note to future generations: prepending ./ is a safety measure to ensure that +# the environment does not malicously set `CLEANFILES` to `\`. +.PHONY: clean +clean: + [ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/* + [ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/* + [ -n "$(UPDATEREPODIR)" ] && [ $(UPDATEREPODIR) != "." ] && [ $(UPDATEREPODIR) != "/" ] && [ $(UPDATEREPODIR) != ".." ] && [ -d ./$(UPDATEREPODIR) ] && rm -rf ./$(UPDATEREPODIR)/* + rm -f $(CLEANFILES) + +.PHONY: help +help: + @echo "$$data" + +define data +Usage: [IMAGE=(odklite|odkfull)] [ODK_DEBUG=yes] sh run.sh make [(IMP|MIR|IMP_LARGE|PAT)=(false|true)] command + +---------------------------------------- + Command reference +---------------------------------------- + +Core commands: +* prepare_release: Run the entire release pipeline. Use make IMP=false prepare_release to avoid rerunning the imports +* prepare_release_fast: Run the entire release pipeline without refreshing imports, recreating components or recompiling patterns. +* update_repo: Update the ODK repository setup using the config file ro-odk.yaml +* test: Running all validation tests +* odkversion: Show the current version of the ODK Makefile and ROBOT. +* clean: Delete all temporary files +* help: Print ODK Usage information +* public_release: Uploads the release file to a release management system, such as GitHub releases. Must be configured. + + +Imports management: +* refresh-imports: Refresh all imports and mirrors. +* recreate-components: Recreate all components. +* no-mirror-refresh-imports: Refresh all imports without downloading mirrors. +* refresh-imports-excluding-large: Refresh all imports and mirrors, but skipping the ones labelled as 'is_large'. +* refresh-%: Refresh a single import, i.e. refresh-go will refresh 'imports/go_import.owl'. +* no-mirror-refresh-%: Refresh a single import without updating the mirror, i.e. refresh-go will refresh 'imports/go_import.owl'. +* mirror-%: Refresh a single mirror. + +Editor utilities: +* validate_idranges: Make sure your ID ranges file is formatted correctly +* normalize_src: Load and safe your ro-edit file after you to make sure its serialised correctly +* explain_unsat: If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes +* validate-all-tsv: Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files +* validate-tsv: Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv. +* release_diff: Create a diff between the current release and the new release + +Additional build commands (advanced users) +* all: Run the entire pipeline (like prepare_release), but without copying the release files to the release directory. +* all_subsets: Build all subsets +* custom_reports: Generate all custom sparql reports you have configured in your ro-odk.yaml file. +* all_assets: Build all assets +* show_assets: Print a list of all assets that would be build by the release pipeline +* all_mappings: Update all SSSOM mapping sets + +Additional QC commands (advanced users) +* robot_reports: Run all configured ROBOT reports +* validate_profile_%: Run an OWL2 DL profile validation check, for example validate_profile_ro-edit.owl. +* reason_test: Run a basic reasoning test + +Examples: +* sh run.sh make IMP=false prepare_release +* sh run.sh make update_repo +* sh run.sh make test + +Tricks: +* Add -B to the end of your command to force re-running it even if nothing has changed +* Use the IMAGE parameter to the run.sh script to use a different image like odklite +* Use ODK_DEBUG=yes sh run.sh make ... to print information about timing and debugging + +endef +export data + +include ro.Makefile \ No newline at end of file diff --git a/src/ontology/annotations.owl b/src/ontology/annotations.owl deleted file mode 100644 index 8f184ce9..00000000 --- a/src/ontology/annotations.owl +++ /dev/null @@ -1,338 +0,0 @@ - - - - - - - - - - - -]> - - - - - - - - - - - - - - - - editor preferred term - - - - - - - - example of usage - - - - - - - - - has curation status - - - - - - - - definition - - - - - - - - - editor note - - - - - - - - - term editor - - - - - - - - - alternative term - - - - - - - - - definition source - - - - - - - - - imported from - - - - - - - - - expand expression to - - - - - - - - expand assertion to - - - - - - - - first order logic expression - - - - - - - - elucidation - - - - - - - - temporal interpretation - https://oborel.github.io/obo-relations/temporal-semantics/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - shorthand - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - axiom holds for all times - - -## Elucidation - -This is used when the statement/axiom is assumed to hold true 'eternally' - -## How to interpret (informal) - -First the "atemporal" FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. - -## Example - - Class: nucleus - SubClassOf: part_of some cell - - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) - -## Notes - -This interpretation is *not* the same as an at-all-times relation - - - - - - - - - - relation has no temporal argument - - -## Elucidation - -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. - -## Example: - - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm - - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y) - - - - - - - - - - - ready for release - - - - - - - - pending final vetting - - - - - - - - requires discussion - - - - - - - - curator note - - - - - - - - diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index f70061fa..bb69da3e 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -1,22 +1,27 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/chemical.owl b/src/ontology/chemical.owl deleted file mode 100644 index 935ce1ce..00000000 --- a/src/ontology/chemical.owl +++ /dev/null @@ -1,39 +0,0 @@ -Prefix(:=) -Prefix(dc:=) -Prefix(obo:=) -Prefix(owl:=) -Prefix(rdf:=) -Prefix(xml:=) -Prefix(xsd:=) -Prefix(cito:=) -Prefix(foaf:=) -Prefix(rdfs:=) -Prefix(swrl:=) -Prefix(swrla:=) -Prefix(swrlb:=) -Prefix(subsets:=) -Prefix(oboInOwl:=) - - -Ontology( -Annotation(dc:description "RO chemical module."@en) - -# Object Property: obo:RO_0002260 (has biological role) - -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002260 "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)") -AnnotationAssertion(rdfs:label obo:RO_0002260 "has biological role") -SubObjectPropertyOf(obo:RO_0002260 obo:RO_0000087) - -# Object Property: obo:RO_0002261 (has application role) - -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002261 "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)") -AnnotationAssertion(rdfs:label obo:RO_0002261 "has application role") -SubObjectPropertyOf(obo:RO_0002261 obo:RO_0000087) - -# Object Property: obo:RO_0002262 (has chemical role) - -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002262 "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)") -AnnotationAssertion(rdfs:label obo:RO_0002262 "has chemical role") -SubObjectPropertyOf(obo:RO_0002262 obo:RO_0000087) - -) \ No newline at end of file diff --git a/src/ontology/bfo-axioms.owl b/src/ontology/components/bfo-axioms.owl similarity index 100% rename from src/ontology/bfo-axioms.owl rename to src/ontology/components/bfo-axioms.owl diff --git a/src/ontology/bfo-classes-minimal.owl b/src/ontology/components/bfo-classes-minimal.owl similarity index 98% rename from src/ontology/bfo-classes-minimal.owl rename to src/ontology/components/bfo-classes-minimal.owl index 7e8b2527..625240e4 100644 --- a/src/ontology/bfo-classes-minimal.owl +++ b/src/ontology/components/bfo-classes-minimal.owl @@ -9,7 +9,7 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - + diff --git a/src/ontology/core.owl b/src/ontology/components/core.owl similarity index 99% rename from src/ontology/core.owl rename to src/ontology/components/core.owl index 227ebb83..2db9cc6a 100644 --- a/src/ontology/core.owl +++ b/src/ontology/components/core.owl @@ -12,9 +12,7 @@ xmlns:swrl="http://www.w3.org/2003/11/swrl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - + https://github.com/oborel/obo-relations/wiki/ROCore @@ -850,4 +848,3 @@ A continuant cannot have an occurrent as part: use 'participates in'. - diff --git a/src/ontology/el-constraints.owl b/src/ontology/components/el-constraints.owl similarity index 97% rename from src/ontology/el-constraints.owl rename to src/ontology/components/el-constraints.owl index be5809d0..3ee9dc50 100644 --- a/src/ontology/el-constraints.owl +++ b/src/ontology/components/el-constraints.owl @@ -21,7 +21,7 @@ xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - + This ontology is intended for encoding constraints on ro/core in a way that is usable by EL reasoners such as Elk. In future this ontology may be derived by some automatic or semi-automatic translation process from a more direct encoding. diff --git a/src/ontology/generated-axioms.owl b/src/ontology/components/generated-axioms.owl similarity index 98% rename from src/ontology/generated-axioms.owl rename to src/ontology/components/generated-axioms.owl index 4adb7c15..bd232206 100644 --- a/src/ontology/generated-axioms.owl +++ b/src/ontology/components/generated-axioms.owl @@ -6,7 +6,7 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - + diff --git a/rohom.owl b/src/ontology/components/rohom.owl similarity index 99% rename from rohom.owl rename to src/ontology/components/rohom.owl index f48e567e..3fbd4fc8 100644 --- a/rohom.owl +++ b/src/ontology/components/rohom.owl @@ -8,7 +8,7 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + 1.2 diff --git a/src/ontology/temporal-intervals.owl b/src/ontology/components/temporal-intervals.owl similarity index 99% rename from src/ontology/temporal-intervals.owl rename to src/ontology/components/temporal-intervals.owl index bb7ee22f..80f04b4d 100644 --- a/src/ontology/temporal-intervals.owl +++ b/src/ontology/components/temporal-intervals.owl @@ -9,7 +9,7 @@ xmlns:obo="http://purl.obolibrary.org/obo/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:dc="http://purl.org/dc/elements/1.1/"> - + diff --git a/src/ontology/go-biotic.owl b/src/ontology/go-biotic.owl deleted file mode 100644 index 8b2ae6ca..00000000 --- a/src/ontology/go-biotic.owl +++ /dev/null @@ -1,15 +0,0 @@ - - - - - - - - - diff --git a/src/ontology/go_cc_import.owl b/src/ontology/go_cc_import.owl deleted file mode 100644 index e98e6ad5..00000000 --- a/src/ontology/go_cc_import.owl +++ /dev/null @@ -1,165 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nucleus - - - - - - - - - biological_process - - - - - - - - - - membrane - - - - - - - - - - axon - - - - - - - - - - dendrite - - - - - - - - - - - presynaptic membrane - - - - - - - - - cell projection - - - - - - - - - - neuron projection - - - - - - - - - synapse part - - - - - - - - - - synapse - - - - - - - - - - - postsynaptic membrane - - - - - - - diff --git a/src/ontology/go_mf_import.owl b/src/ontology/go_mf_import.owl deleted file mode 100644 index 1f81d784..00000000 --- a/src/ontology/go_mf_import.owl +++ /dev/null @@ -1,116 +0,0 @@ - - - - - - - - - - - - - - - molecular_function - - - - - - - - catalytic activity - - - - - - - - - ubiquitin-protein ligase activity - - - - - - - - - kinase activity - - - - - - - - - transferase activity - - - - - - - - - transferase activity, transferring phosphorus-containing groups - - - - - - - - - ligase activity - - - - - - - - - ligase activity, forming carbon-nitrogen bonds - - - - - - - - - acid-amino acid ligase activity - - - - - - - - - small conjugating protein ligase activity - - - - - - - - - diff --git a/src/ontology/imports/caro_import.owl b/src/ontology/imports/caro_import.owl new file mode 100644 index 00000000..2de45160 --- /dev/null +++ b/src/ontology/imports/caro_import.owl @@ -0,0 +1,112 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( "None") +Annotation( ) +Annotation( "Common Anatomy Reference Ontology") +Annotation( ) +Annotation(rdfs:comment "Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendal.") +Annotation(owl:versionInfo "2022-02-18") +Annotation(owl:versionInfo "2023-02-19") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) + + + +############################ +# Classes +############################ + +# Class: (anatomical entity) + +AnnotationAssertion(Annotation( "CAROC:Brownsville2014") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") +AnnotationAssertion( "CARO:0000000") +AnnotationAssertion(rdfs:comment "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.") +AnnotationAssertion(rdfs:label "anatomical entity") +SubClassOf( ) + +# Class: (connected anatomical structure) + +AnnotationAssertion( "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.") +AnnotationAssertion( "CARO:0000003") +AnnotationAssertion(rdfs:comment "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development.") +AnnotationAssertion(rdfs:label "connected anatomical structure") +SubClassOf( ) + +# Class: (material anatomical entity) + +AnnotationAssertion( "An anatomical entity that has mass.") +AnnotationAssertion( "CARO:0000006") +AnnotationAssertion(rdfs:label "material anatomical entity") +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (immaterial anatomical entity) + +AnnotationAssertion( "Anatomical entity that has no mass.") +AnnotationAssertion( "CARO:0000007") +AnnotationAssertion(rdfs:label "immaterial anatomical entity") +SubClassOf( ) +SubClassOf( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (neuron projection bundle) + +AnnotationAssertion( "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.") +AnnotationAssertion( "CARO:0001001") +AnnotationAssertion(rdfs:label "neuron projection bundle") +SubClassOf( ) + +# Class: (organism or virus or viroid) + +AnnotationAssertion( "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.") +AnnotationAssertion( "Melissa Haendel") +AnnotationAssertion(rdfs:label "organism or virus or viroid") +SubClassOf( ) + +# Class: (multicellular anatomical structure) + +AnnotationAssertion( "An anatomical structure that has more than one cell as a part.") +AnnotationAssertion( "djs93") +AnnotationAssertion( "CARO:0010000") +AnnotationAssertion(rdfs:label "multicellular anatomical structure") +SubClassOf( ) +SubClassOf( ) + + +) \ No newline at end of file diff --git a/src/ontology/imports/caro_terms.txt b/src/ontology/imports/caro_terms.txt new file mode 100644 index 00000000..2861c295 --- /dev/null +++ b/src/ontology/imports/caro_terms.txt @@ -0,0 +1,6 @@ +CARO:0000003 +CARO:0001001 +CARO:0000006 +CARO:0000000 +CARO:0001010 +CARO:0000007 diff --git a/src/ontology/imports/cl_import.owl b/src/ontology/imports/cl_import.owl new file mode 100644 index 00000000..45f795ab --- /dev/null +++ b/src/ontology/imports/cl_import.owl @@ -0,0 +1,100 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation( "An ontology of cell types.") +Annotation( ) +Annotation( "Cell Ontology") +Annotation( ) +Annotation( ) +Annotation( ) +Annotation( ) +Annotation( ) +Annotation( ) +Annotation( ) +Annotation( ) +Annotation( ) +Annotation( ) +Annotation(rdfs:comment "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo.") +Annotation(owl:versionInfo "2023-02-19") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) + + + +############################ +# Classes +############################ + +# Class: (cell) + +AnnotationAssertion(Annotation( "CARO:mah") "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") +AnnotationAssertion( "CALOHA:TS-2035") +AnnotationAssertion( "FBbt:00007002") +AnnotationAssertion( "FMA:68646") +AnnotationAssertion( "GO:0005623") +AnnotationAssertion( "KUPO:0000002") +AnnotationAssertion( "MESH:D002477") +AnnotationAssertion( "VHOG:0001533") +AnnotationAssertion( "WBbt:0004017") +AnnotationAssertion( "XAO:0003012") +AnnotationAssertion(rdfs:comment "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).") +AnnotationAssertion(rdfs:label "cell") + +# Class: (sensory neuron) + +AnnotationAssertion(Annotation( "ISBN:0721662544") "Any neuron having a sensory function; an afferent neuron conveying sensory impulses.") +AnnotationAssertion( "BTO:0001037") +AnnotationAssertion( "FBbt:00005124") +AnnotationAssertion( "FMA:84649") +AnnotationAssertion( "MESH:D011984") +AnnotationAssertion( "WBbt:0005759") +AnnotationAssertion(rdfs:label "sensory neuron") +SubClassOf( ) + +# Class: (neuron) + +AnnotationAssertion(Annotation( "MESH:D009474") Annotation( "http://en.wikipedia.org/wiki/Neuron") "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.") +AnnotationAssertion( ) +AnnotationAssertion( "BTO:0000938") +AnnotationAssertion( "CALOHA:TS-0683") +AnnotationAssertion( "FBbt:00005106") +AnnotationAssertion( "FMA:54527") +AnnotationAssertion( "VHOG:0001483") +AnnotationAssertion( "WBbt:0003679") +AnnotationAssertion( "nerve cell") +AnnotationAssertion(rdfs:comment "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.") +AnnotationAssertion(rdfs:label "neuron") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + + +) \ No newline at end of file diff --git a/src/ontology/imports/cl_terms.txt b/src/ontology/imports/cl_terms.txt new file mode 100644 index 00000000..406e1951 --- /dev/null +++ b/src/ontology/imports/cl_terms.txt @@ -0,0 +1,3 @@ +CL:0000000 +CL:0000540 +CL:0000101 \ No newline at end of file diff --git a/src/ontology/imports/envo_import.owl b/src/ontology/imports/envo_import.owl new file mode 100644 index 00000000..87a298c6 --- /dev/null +++ b/src/ontology/imports/envo_import.owl @@ -0,0 +1,125 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation( ) +Annotation( "http://orcid.org/0000-0002-6601-2165") +Annotation( "http://orcid.org/0000-0002-8343-612X") +Annotation( "http://orcid.org/0000-0003-1604-1512") +Annotation( "ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities") +Annotation( ) +Annotation( "The Environment Ontology") +Annotation( ) +Annotation( "https://github.com/EnvironmentOntology/envo/"^^xsd:anyURI) +Annotation( "https://github.com/EnvironmentOntology/envo/issues/"^^xsd:anyURI) +Annotation( "ENVO") +Annotation(rdfs:comment "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 679 Logical Axioms: 119]") +Annotation(rdfs:comment "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 206 Logical Axioms: 34]") +Annotation(rdfs:comment "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 168 Logical Axioms: 29]") +Annotation(rdfs:comment "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 40 Logical Axioms: 6]") +Annotation(rdfs:comment "Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 21 Logical Axioms: 2]") +Annotation(owl:versionInfo "2023-02-13") +Annotation(owl:versionInfo "2023-02-19") +Annotation( "http://environmentontology.org/"^^xsd:anyURI) + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) + +############################ +# Object Properties +############################ + +# Object Property: (derives from part of) + +AnnotationAssertion( "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity."@en) +AnnotationAssertion(rdfs:label "derives from part of"@en) + + + +############################ +# Classes +############################ + +# Class: (environmental system) + +AnnotationAssertion(Annotation( "DOI:10.1186/2041-1480-4-43") "A system which has the disposition to environ one or more material entities.") +AnnotationAssertion( "2013-09-23T16:04:08Z") +AnnotationAssertion( "EcoLexicon:environment") +AnnotationAssertion( "environment") +AnnotationAssertion(rdfs:comment "In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class \"system\". The relation \"environed_by\" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.") +AnnotationAssertion(rdfs:label "environmental system") +SubClassOf( ) + + +) \ No newline at end of file diff --git a/src/ontology/imports/envo_terms.txt b/src/ontology/imports/envo_terms.txt new file mode 100644 index 00000000..43e38d61 --- /dev/null +++ b/src/ontology/imports/envo_terms.txt @@ -0,0 +1 @@ +ENVO:01000254 diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl new file mode 100644 index 00000000..4ff3b62f --- /dev/null +++ b/src/ontology/imports/go_import.owl @@ -0,0 +1,238 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( "The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.") +Annotation( ) +Annotation( "Gene Ontology") +Annotation( ) +Annotation( "gene_ontology") +Annotation( "1.2") +Annotation(owl:versionInfo "2023-01-01") +Annotation(owl:versionInfo "2023-02-19") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) + + + +############################ +# Classes +############################ + +# Class: (molecular_function) + +AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.") +AnnotationAssertion( "molecular function") +AnnotationAssertion( "GO:0003674") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") +AnnotationAssertion(rdfs:label "molecular_function") + +# Class: (ubiquitin-protein transferase activity) + +AnnotationAssertion(Annotation( "GOC:BioGRID") Annotation( "GOC:jh2") Annotation( "PMID:9635407") "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.") +AnnotationAssertion( "KEGG_REACTION:R03876") +AnnotationAssertion(Annotation(rdfs:label "ISGylation of IRF3") "Reactome:R-HSA-1169394") +AnnotationAssertion(Annotation(rdfs:label "ISGylation of viral protein NS1") "Reactome:R-HSA-1169395") +AnnotationAssertion(Annotation(rdfs:label "Activation of ISG15 by UBA7 E1 ligase") "Reactome:R-HSA-1169397") +AnnotationAssertion(Annotation(rdfs:label "ISGylation of host protein filamin B") "Reactome:R-HSA-1169398") +AnnotationAssertion(Annotation(rdfs:label "ISGylation of E2 conjugating enzymes") "Reactome:R-HSA-1169402") +AnnotationAssertion(Annotation(rdfs:label "ISGylation of protein phosphatase 1 beta (PP2CB)") "Reactome:R-HSA-1169405") +AnnotationAssertion(Annotation(rdfs:label "ISGylation of host proteins") "Reactome:R-HSA-1169406") +AnnotationAssertion(Annotation(rdfs:label "Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha") "Reactome:R-HSA-1234163") +AnnotationAssertion(Annotation(rdfs:label "Nuclear VBC complex ubiquitinylates HIF-alpha") "Reactome:R-HSA-1234172") +AnnotationAssertion(Annotation(rdfs:label "ERBB4 ubiquitination by WWP1/ITCH") "Reactome:R-HSA-1253282") +AnnotationAssertion(Annotation(rdfs:label "Self-ubiquitination of RNF41") "Reactome:R-HSA-1358789") +AnnotationAssertion(Annotation(rdfs:label "RNF41 ubiquitinates ERBB3") "Reactome:R-HSA-1358790") +AnnotationAssertion(Annotation(rdfs:label "RNF41 ubiquitinates activated ERBB3") "Reactome:R-HSA-1358792") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of p130 (RBL2) by SCF (Skp2)") "Reactome:R-HSA-1363331") +AnnotationAssertion(Annotation(rdfs:label "K63-linked ubiquitination of RIP1 bound to the activated TLR complex") "Reactome:R-HSA-168915") +AnnotationAssertion(Annotation(rdfs:label "SMURF2 ubiquitinates SMAD2") "Reactome:R-HSA-173542") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling") "Reactome:R-HSA-173545") +AnnotationAssertion(Annotation(rdfs:label "Multiubiquitination of APC/C-associated Cdh1") "Reactome:R-HSA-174057") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of Cyclin A by APC/C:Cdc20 complex") "Reactome:R-HSA-174104") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of Securin by phospho-APC/C:Cdc20 complex") "Reactome:R-HSA-174144") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of Emi1 by SCF-beta-TrCP") "Reactome:R-HSA-174159") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex") "Reactome:R-HSA-174195") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex") "Reactome:R-HSA-174227") +AnnotationAssertion(Annotation(rdfs:label "Multiubiquitination of Nek2A") "Reactome:R-HSA-179417") +AnnotationAssertion(Annotation(rdfs:label "Multi-ubiquitination of APOBEC3G") "Reactome:R-HSA-180540") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex") "Reactome:R-HSA-180597") +AnnotationAssertion(Annotation(rdfs:label "CBL-mediated ubiquitination of CIN85") "Reactome:R-HSA-182986") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of stimulated EGFR (CBL)") "Reactome:R-HSA-182993") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of stimulated EGFR (CBL:GRB2)") "Reactome:R-HSA-183036") +AnnotationAssertion(Annotation(rdfs:label "CBL ubiquitinates Sprouty") "Reactome:R-HSA-183051") +AnnotationAssertion(Annotation(rdfs:label "CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix") "Reactome:R-HSA-183084") +AnnotationAssertion(Annotation(rdfs:label "CBL binds and ubiquitinates phosphorylated Sprouty") "Reactome:R-HSA-183089") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of NICD1 by FBWX7") "Reactome:R-HSA-1852623") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of phospho-p27/p21") "Reactome:R-HSA-187575") +AnnotationAssertion(Annotation(rdfs:label "ITCH ubiquitinates DTX") "Reactome:R-HSA-1912357") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of NOTCH1 by ITCH in the absence of ligand") "Reactome:R-HSA-1912386") +AnnotationAssertion(Annotation(rdfs:label "CHIP (STUB1) mediates ubiquitination of ERBB2") "Reactome:R-HSA-1918092") +AnnotationAssertion(Annotation(rdfs:label "CUL5 mediates ubiquitination of ERBB2") "Reactome:R-HSA-1918095") +AnnotationAssertion(Annotation(rdfs:label "NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer") "Reactome:R-HSA-1977296") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1") "Reactome:R-HSA-1980074") +AnnotationAssertion(Annotation(rdfs:label "ARRB mediates NOTCH1 ubiquitination") "Reactome:R-HSA-1980118") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling") "Reactome:R-HSA-201425") +AnnotationAssertion(Annotation(rdfs:label "Auto-ubiquitination of TRAF6") "Reactome:R-HSA-202453") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of NEMO by TRAF6") "Reactome:R-HSA-202534") +AnnotationAssertion(Annotation(rdfs:label "TRAF6 polyubiquitinates NRIF") "Reactome:R-HSA-205118") +AnnotationAssertion(Annotation(rdfs:label "Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex") "Reactome:R-HSA-209063") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of PAK-2p34") "Reactome:R-HSA-211734") +AnnotationAssertion(Annotation(rdfs:label "SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7") "Reactome:R-HSA-2169050") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of DLL/JAG ligands upon binding to NOTCH2") "Reactome:R-HSA-2172172") +AnnotationAssertion(Annotation(rdfs:label "SMURF2 monoubiquitinates SMAD3") "Reactome:R-HSA-2179276") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of SKI/SKIL by RNF111/SMURF2") "Reactome:R-HSA-2186747") +AnnotationAssertion(Annotation(rdfs:label "RNF111 ubiquitinates SMAD7") "Reactome:R-HSA-2186785") +AnnotationAssertion(Annotation(rdfs:label "STUB1 (CHIP) ubiquitinates SMAD3") "Reactome:R-HSA-2187368") +AnnotationAssertion(Annotation(rdfs:label "Auto-ubiquitination of TRAF3") "Reactome:R-HSA-2213017") +AnnotationAssertion(Annotation(rdfs:label "Autoubiquitination of phospho-COP1(Ser-387 )") "Reactome:R-HSA-264444") +AnnotationAssertion(Annotation(rdfs:label "RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels") "Reactome:R-HSA-2682349") +AnnotationAssertion(Annotation(rdfs:label "Auto-ubiquitination of TRAF6") "Reactome:R-HSA-2730904") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants") "Reactome:R-HSA-2737728") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants") "Reactome:R-HSA-2769007") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants") "Reactome:R-HSA-2900765") +AnnotationAssertion(Annotation(rdfs:label "SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA") "Reactome:R-HSA-3000335") +AnnotationAssertion(Annotation(rdfs:label "STING ubiquitination by TRIM32 or TRIM56") "Reactome:R-HSA-3134804") +AnnotationAssertion(Annotation(rdfs:label "DDX41 ubiquitination by TRIM21") "Reactome:R-HSA-3134946") +AnnotationAssertion(Annotation(rdfs:label "DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1") "Reactome:R-HSA-3249386") +AnnotationAssertion(Annotation(rdfs:label "NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2") "Reactome:R-HSA-3780995") +AnnotationAssertion(Annotation(rdfs:label "NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1") "Reactome:R-HSA-3781009") +AnnotationAssertion(Annotation(rdfs:label "Cdh1:APC/C ubiquitinates EHMT1 and EHMT2") "Reactome:R-HSA-3788724") +AnnotationAssertion(Annotation(rdfs:label "Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease)") "Reactome:R-HSA-3797226") +AnnotationAssertion(Annotation(rdfs:label "BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins") "Reactome:R-HSA-400267") +AnnotationAssertion(Annotation(rdfs:label "CBL neddylates TGFBR2") "Reactome:R-HSA-4332236") +AnnotationAssertion(Annotation(rdfs:label "TRAF6 is K63 poly-ubiquitinated") "Reactome:R-HSA-446877") +AnnotationAssertion(Annotation(rdfs:label "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation") "Reactome:R-HSA-450358") +AnnotationAssertion(Annotation(rdfs:label "Pellino ubiquitinates IRAK1") "Reactome:R-HSA-451418") +AnnotationAssertion(Annotation(rdfs:label "Parkin promotes the ubiquitination of mitochondrial substrates") "Reactome:R-HSA-5205682") +AnnotationAssertion(Annotation(rdfs:label "BIRC(cIAP1/2) ubiquitinates RIPK1") "Reactome:R-HSA-5357757") +AnnotationAssertion(Annotation(rdfs:label "SYVN1 ubiquitinates Hh C-terminal fragments") "Reactome:R-HSA-5362412") +AnnotationAssertion(Annotation(rdfs:label "Hh processing variants are ubiquitinated") "Reactome:R-HSA-5483238") +AnnotationAssertion(Annotation(rdfs:label "SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP") "Reactome:R-HSA-5607725") +AnnotationAssertion(Annotation(rdfs:label "beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex") "Reactome:R-HSA-5607728") +AnnotationAssertion(Annotation(rdfs:label "TRAF6 oligomer autoubiquitinates") "Reactome:R-HSA-5607756") +AnnotationAssertion(Annotation(rdfs:label "K63polyUb-TRAF6 ubiquitinates TAK1") "Reactome:R-HSA-5607757") +AnnotationAssertion(Annotation(rdfs:label "SCF(beta-TrCP) ubiquitinates p-GLI1") "Reactome:R-HSA-5610742") +AnnotationAssertion(Annotation(rdfs:label "SCF(beta-TrCP) ubiquitinates p-GLI2") "Reactome:R-HSA-5610745") +AnnotationAssertion(Annotation(rdfs:label "SCF(beta-TrCP) ubiquitinates p-GLI3") "Reactome:R-HSA-5610746") +AnnotationAssertion(Annotation(rdfs:label "RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA") "Reactome:R-HSA-5652009") +AnnotationAssertion(Annotation(rdfs:label "RCHY1 monoubiquitinates POLH") "Reactome:R-HSA-5655170") +AnnotationAssertion(Annotation(rdfs:label "SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA") "Reactome:R-HSA-5660753") +AnnotationAssertion(Annotation(rdfs:label "SIAH1, SIAH2 ubiquitinate SNCAIP") "Reactome:R-HSA-5667107") +AnnotationAssertion(Annotation(rdfs:label "PARK2 K63-Ubiquitinates SNCAIP") "Reactome:R-HSA-5667111") +AnnotationAssertion(Annotation(rdfs:label "K63polyUb-cIAP1,2 ubiquitinates TRAF3") "Reactome:R-HSA-5668454") +AnnotationAssertion(Annotation(rdfs:label "cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK") "Reactome:R-HSA-5668534") +AnnotationAssertion(Annotation(rdfs:label "BIRC2/3 (cIAP1/2) is autoubiquitinated") "Reactome:R-HSA-5675470") +AnnotationAssertion(Annotation(rdfs:label "SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2") "Reactome:R-HSA-5684250") +AnnotationAssertion(Annotation(rdfs:label "SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2") "Reactome:R-HSA-5691108") +AnnotationAssertion(Annotation(rdfs:label "TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains") "Reactome:R-HSA-5693108") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of phosphorylated Cdc25A") "Reactome:R-HSA-69598") +AnnotationAssertion(Annotation(rdfs:label "RIP2 induces K63-linked ubiquitination of NEMO") "Reactome:R-HSA-741386") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of Cyclin D1") "Reactome:R-HSA-75824") +AnnotationAssertion(Annotation(rdfs:label "TRIM33 monoubiquitinates SMAD4") "Reactome:R-HSA-870449") +AnnotationAssertion(Annotation(rdfs:label "DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3") "Reactome:R-HSA-8948709") +AnnotationAssertion(Annotation(rdfs:label "VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha") "Reactome:R-HSA-8956106") +AnnotationAssertion(Annotation(rdfs:label "Ubiquitination of DLL/JAG ligands upon binding to NOTCH3") "Reactome:R-HSA-9013069") +AnnotationAssertion(Annotation(rdfs:label "Auto-ubiquitination of TRAF3 within activated TLR3 complex") "Reactome:R-HSA-9013974") +AnnotationAssertion(Annotation(rdfs:label "K63-linked ubiquitination of RIP1 bound to the activated TLR complex") "Reactome:R-HSA-9014342") +AnnotationAssertion(Annotation(rdfs:label "DDX58 is K63 polyubiquitinated") "Reactome:R-HSA-918224") +AnnotationAssertion(Annotation(rdfs:label "RNF125 mediated ubiquitination of DDX58, IFIH1 and MADS") "Reactome:R-HSA-936412") +AnnotationAssertion(Annotation(rdfs:label "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2") "Reactome:R-HSA-936942") +AnnotationAssertion(Annotation(rdfs:label "Activated TRAF6 synthesizes unanchored polyubiquitin chains") "Reactome:R-HSA-936986") +AnnotationAssertion(Annotation(rdfs:label "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation") "Reactome:R-HSA-9628444") +AnnotationAssertion(Annotation(rdfs:label "Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation") "Reactome:R-HSA-9645394") +AnnotationAssertion(Annotation(rdfs:label "Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer") "Reactome:R-HSA-9645414") +AnnotationAssertion(Annotation(rdfs:label "STUB1 ubiquitinates RIPK3 at K55, K363") "Reactome:R-HSA-9688831") +AnnotationAssertion(Annotation(rdfs:label "BRCA1:BARD1 heterodimer autoubiquitinates") "Reactome:R-HSA-9701000") +AnnotationAssertion(Annotation(rdfs:label "TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex") "Reactome:R-HSA-975118") +AnnotationAssertion(Annotation(rdfs:label "Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane") "Reactome:R-HSA-975147") +AnnotationAssertion(Annotation(rdfs:label "Transfer of Ub from E2 to substrate and release of E2") "Reactome:R-HSA-983140") +AnnotationAssertion(Annotation(rdfs:label "E1 mediated ubiquitin activation") "Reactome:R-HSA-983153") +AnnotationAssertion(Annotation(rdfs:label "Polyubiquitination of substrate") "Reactome:R-HSA-983156") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "anaphase-promoting complex activity") +AnnotationAssertion( "ubiquitin conjugating enzyme activity") +AnnotationAssertion( "ubiquitin ligase activity") +AnnotationAssertion( "ubiquitin protein ligase activity") +AnnotationAssertion( "ubiquitin protein-ligase activity") +AnnotationAssertion( "ubiquitin-conjugating enzyme activity") +AnnotationAssertion( "E2") +AnnotationAssertion( "E3") +AnnotationAssertion( "GO:0004842") +AnnotationAssertion(rdfs:label "ubiquitin-protein transferase activity") +SubClassOf( ) + +# Class: (nucleus) + +AnnotationAssertion(Annotation( "GOC:go_curators") "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.") +AnnotationAssertion( "NIF_Subcellular:sao1702920020") +AnnotationAssertion( "Wikipedia:Cell_nucleus") +AnnotationAssertion( "cell nucleus") +AnnotationAssertion(Annotation( "GOC:al") Annotation( "GOC:mah") Annotation( "GOC:vw") Annotation( "PMID:15030757") "horsetail nucleus") +AnnotationAssertion( "GO:0005634") +AnnotationAssertion(rdfs:label "nucleus") + +# Class: (biological_process) + +AnnotationAssertion(Annotation( "GOC:pdt") "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-19T15:05:24Z") +AnnotationAssertion( "Wikipedia:Biological_process") +AnnotationAssertion( "biological process") +AnnotationAssertion( "physiological process") +AnnotationAssertion( "single organism process") +AnnotationAssertion( "single-organism process") +AnnotationAssertion( "GO:0008150") +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") +AnnotationAssertion(rdfs:label "biological_process") + +# Class: (kinase activity) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") +AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") +AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") +AnnotationAssertion( "phosphokinase activity") +AnnotationAssertion( "GO:0016301") +AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") +AnnotationAssertion(rdfs:label "kinase activity") +SubClassOf( ) + +# Class: (myristoyltransferase activity) + +AnnotationAssertion(Annotation( "GOC:ai") "Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.") +AnnotationAssertion(Annotation(rdfs:label "Myristoylation of tBID by NMT1") "Reactome:R-HSA-141367") +AnnotationAssertion(Annotation(rdfs:label "Myristoylation of Nef") "Reactome:R-HSA-162914") +AnnotationAssertion( "GO:0019107") +AnnotationAssertion(rdfs:label "myristoyltransferase activity") +SubClassOf( ) + + +) \ No newline at end of file diff --git a/src/ontology/imports/go_terms.txt b/src/ontology/imports/go_terms.txt new file mode 100644 index 00000000..a125f9f5 --- /dev/null +++ b/src/ontology/imports/go_terms.txt @@ -0,0 +1,5 @@ +GO:0008150 +GO:0005634 +GO:0019107 +GO:0004842 +GO:0016301 \ No newline at end of file diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl new file mode 100644 index 00000000..5031c561 --- /dev/null +++ b/src/ontology/imports/omo_import.owl @@ -0,0 +1,54 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2023-02-19") + +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (defined by construct) + +AnnotationAssertion( "'part disjoint with' 'defined by construct' \"\"\" + PREFIX owl: + PREFIX : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "defined by construct") + + + +) \ No newline at end of file diff --git a/src/ontology/imports/omo_terms.txt b/src/ontology/imports/omo_terms.txt new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/src/ontology/imports/omo_terms.txt @@ -0,0 +1 @@ + diff --git a/src/ontology/imports/other_import.owl b/src/ontology/imports/other_import.owl new file mode 100644 index 00000000..d7cfd7ce --- /dev/null +++ b/src/ontology/imports/other_import.owl @@ -0,0 +1,67 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( +Annotation(rdfs:comment "Ad-hoc additional imports, manually copied. This should be split into several dynamically imported sub-modules.") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (OBO foundry unique label) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "OBO foundry unique label"@en) + + + + +############################ +# Classes +############################ + +# Class: (disease) + +AnnotationAssertion( "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism."@en) +AnnotationAssertion(rdfs:label "disease") +SubClassOf( ) + +# Class: (phenotype) + +AnnotationAssertion(rdfs:label "phenotype"@en) +SubClassOf( ) + + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "ready for release"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "pending final vetting"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "requires discussion"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "term replaced by"@en) +) \ No newline at end of file diff --git a/src/ontology/imports/other_terms.txt b/src/ontology/imports/other_terms.txt new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/src/ontology/imports/other_terms.txt @@ -0,0 +1 @@ + diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl new file mode 100644 index 00000000..5380ec89 --- /dev/null +++ b/src/ontology/imports/pato_import.owl @@ -0,0 +1,83 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation( "An ontology of phenotypic qualities (properties, attributes or characteristics).") +Annotation( ) +Annotation( "PATO - the Phenotype And Trait Ontology") +Annotation( ) +Annotation( "quality") +Annotation( "1.2") +Annotation(owl:versionInfo "2023-02-17") +Annotation(owl:versionInfo "2023-02-19") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) + + +############################ +# Classes +############################ + +# Class: (quality) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") +AnnotationAssertion( "PATO:0000001") +AnnotationAssertion(rdfs:label "quality") +SubClassOf( ) + +# Class: (branched) + +AnnotationAssertion(Annotation( "WordNet:WordNet") "A branchiness quality inhering in a bearer by virtue of the bearer's having branches.") +AnnotationAssertion( ) +AnnotationAssertion( "ramified") +AnnotationAssertion( "ramiform") +AnnotationAssertion( "PATO:0000402") +AnnotationAssertion(rdfs:label "branched") +SubClassOf( ) + +# Class: (linear) + +AnnotationAssertion(Annotation( "ISBN:0881923214") "A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.") +AnnotationAssertion( "PATO:0001199") +AnnotationAssertion(rdfs:label "linear") +SubClassOf( ) + +# Class: (laminar) + +AnnotationAssertion(Annotation( "PATOC:GVG") "A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer.") +AnnotationAssertion( ) +AnnotationAssertion( "2009-10-06T04:37:14Z") +AnnotationAssertion( "PATO:0002124") +AnnotationAssertion(rdfs:label "laminar") +SubClassOf( ) + + +) \ No newline at end of file diff --git a/src/ontology/imports/pato_terms.txt b/src/ontology/imports/pato_terms.txt new file mode 100644 index 00000000..ce1ec8e4 --- /dev/null +++ b/src/ontology/imports/pato_terms.txt @@ -0,0 +1,4 @@ +PATO:0002124 +PATO:0001199 +PATO:0000402 +PATO:0000001 \ No newline at end of file diff --git a/src/ontology/other_import.owl b/src/ontology/other_import.owl deleted file mode 100644 index 3821c591..00000000 --- a/src/ontology/other_import.owl +++ /dev/null @@ -1,378 +0,0 @@ - - - - This should be split into sub-modules - ad-hoc additional imports - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - OBO foundry unique label - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - anatomical entity - - - - - - - - connected anatomical structure - - - - - - - - - - - material anatomical entity - - - - - - - - - immaterial anatomical entity - - - - - - - - - - connected anatomical system - - - - - - - - - - multi-cell-part structure - - - - - - - - - - neuron projection bundle - - - - - - - - - organism or virus or viroid - - - - - - - - biological entity - - - - - - - - - - - - - - - multicellular anatomical structure - - - - - - - - - - - - - - - - cell - - - - - - - - - - neuron - - - - - - - - - biome - - - - - - - - - environmental system - - - - - - - - - molecular process - - - - - - - - - A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. - disease - - - - - - - - - quality (PATO) - - - - - - - - - - - - - - - - - shape - - - - - - - - - branched - - - - - - - - - branchiness - - - - - - - - - - - - - - - phenotype - - - - - - - - - curation status specification - - - ready for release - - - - - pending final vetting - - - - obsolescence reason specification - - - requires discussion - - - - - term replaced by - - - - - - - diff --git a/src/ontology/pato_import.owl b/src/ontology/pato_import.owl deleted file mode 100644 index 7bad5f16..00000000 --- a/src/ontology/pato_import.owl +++ /dev/null @@ -1,93 +0,0 @@ - - - - - - - - - - - - - - - - - quality - - - - - - - - morphology - - - - - - - - - shape - - - - - - - - - structure - - - - - - - - - linear - - - - - - - - - physical object quality - - - - - - - - - laminar - - - - - - - - - - diff --git a/src/ontology/profile.txt b/src/ontology/profile.txt new file mode 100644 index 00000000..5d9ef49c --- /dev/null +++ b/src/ontology/profile.txt @@ -0,0 +1,25 @@ +WARN annotation_whitespace +ERROR deprecated_boolean_datatype +ERROR deprecated_class_reference +ERROR deprecated_property_reference +ERROR duplicate_definition +WARN duplicate_exact_synonym +WARN duplicate_label_synonym +ERROR duplicate_label +WARN duplicate_scoped_synonym +WARN equivalent_pair +WARN invalid_xref +ERROR label_formatting +ERROR label_whitespace +INFO lowercase_definition +WARN missing_definition +ERROR missing_label +WARN missing_obsolete_label +ERROR missing_ontology_description +ERROR missing_ontology_license +ERROR missing_ontology_title +INFO missing_superclass +ERROR misused_obsolete_label +ERROR multiple_definitions +ERROR multiple_equivalent_classes +ERROR multiple_labels diff --git a/src/ontology/ro-edit.owl b/src/ontology/ro-edit.owl index b1419798..e7220093 100644 --- a/src/ontology/ro-edit.owl +++ b/src/ontology/ro-edit.owl @@ -18,35 +18,36 @@ Prefix(oboInOwl:=) Ontology( -Import() -Import() -Import() -Import() -Import() -Import() -Import() -Import() -Import() -Import() -Import() -Import() -Import() +Import() +Import() +Import() +Import() +Import() +Import() +Import() +Import() +Import() +Import() +Import() +Import() Annotation(dce:description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies."@en) Annotation(dce:title "OBO Relations Ontology"@en) Annotation(dc:license ) Annotation(foaf:homepage " https://github.com/oborel/obo-relations/"^^xsd:anyURI) +Declaration(Class(obo:BFO_0000019)) +Declaration(Class(obo:BFO_0000031)) Declaration(Class(obo:CHEBI_50906)) -Declaration(Class(obo:CL_0000101)) -Declaration(Class(obo:GO_0004872)) -Declaration(Class(obo:GO_0019107)) +Declaration(Class(obo:OGMS_0000031)) Declaration(Class(obo:RO_0002310)) Declaration(Class(obo:RO_0002532)) Declaration(Class(obo:RO_0002533)) Declaration(Class(obo:RO_0002534)) +Declaration(Class(obo:UPHENO_0001001)) Declaration(Class(foaf:image)) Declaration(ObjectProperty(obo:BFO_0000050)) Declaration(ObjectProperty(obo:BFO_0000051)) +Declaration(ObjectProperty(obo:RO_0000058)) Declaration(ObjectProperty(obo:RO_0000300)) Declaration(ObjectProperty(obo:RO_0000301)) Declaration(ObjectProperty(obo:RO_0000302)) @@ -56,6 +57,7 @@ Declaration(ObjectProperty(obo:RO_0001020)) Declaration(ObjectProperty(obo:RO_0001021)) Declaration(ObjectProperty(obo:RO_0001022)) Declaration(ObjectProperty(obo:RO_0001023)) +Declaration(ObjectProperty(obo:RO_0002000)) Declaration(ObjectProperty(obo:RO_0002001)) Declaration(ObjectProperty(obo:RO_0002003)) Declaration(ObjectProperty(obo:RO_0002004)) @@ -81,6 +83,7 @@ Declaration(ObjectProperty(obo:RO_0002023)) Declaration(ObjectProperty(obo:RO_0002024)) Declaration(ObjectProperty(obo:RO_0002025)) Declaration(ObjectProperty(obo:RO_0002026)) +Declaration(ObjectProperty(obo:RO_0002082)) Declaration(ObjectProperty(obo:RO_0002085)) Declaration(ObjectProperty(obo:RO_0002100)) Declaration(ObjectProperty(obo:RO_0002101)) @@ -142,6 +145,7 @@ Declaration(ObjectProperty(obo:RO_0002219)) Declaration(ObjectProperty(obo:RO_0002220)) Declaration(ObjectProperty(obo:RO_0002221)) Declaration(ObjectProperty(obo:RO_0002222)) +Declaration(ObjectProperty(obo:RO_0002223)) Declaration(ObjectProperty(obo:RO_0002225)) Declaration(ObjectProperty(obo:RO_0002226)) Declaration(ObjectProperty(obo:RO_0002227)) @@ -574,12 +578,22 @@ Declaration(ObjectProperty(obo:RO_0019002)) Declaration(ObjectProperty(obo:RO_0019501)) Declaration(ObjectProperty(obo:RO_0040035)) Declaration(ObjectProperty(obo:RO_0040036)) +Declaration(ObjectProperty(obo:RO_HOM0000000)) +Declaration(ObjectProperty(obo:RO_HOM0000001)) +Declaration(ObjectProperty(obo:RO_HOM0000003)) Declaration(DataProperty(obo:RO_0002029)) +Declaration(NamedIndividual(obo:RO_0001901)) +Declaration(NamedIndividual(obo:RO_0001902)) +Declaration(AnnotationProperty(obo:IAO_0000111)) Declaration(AnnotationProperty(obo:IAO_0000115)) Declaration(AnnotationProperty(obo:IAO_0000232)) +Declaration(AnnotationProperty(obo:IAO_0000424)) +Declaration(AnnotationProperty(obo:IAO_0000425)) +Declaration(AnnotationProperty(obo:IAO_0000426)) Declaration(AnnotationProperty(obo:IAO_0000589)) Declaration(AnnotationProperty(obo:IAO_0100001)) Declaration(AnnotationProperty(obo:OMO_0002000)) +Declaration(AnnotationProperty(obo:RO_0001900)) Declaration(AnnotationProperty(obo:RO_0002161)) Declaration(AnnotationProperty(obo:RO_0002171)) Declaration(AnnotationProperty(obo:RO_0002172)) @@ -667,7 +681,7 @@ Declaration(AnnotationProperty(skos:closeMatch)) # Annotation Properties ############################ -# Annotation Property: obo:IAO_0000426 (first order logic expression) +# Annotation Property: obo:IAO_0000426 (obo:IAO_0000426) AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000426 "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property.") SubAnnotationPropertyOf(obo:IAO_0000426 obo:RO_0002422) @@ -675,6 +689,7 @@ SubAnnotationPropertyOf(obo:IAO_0000426 obo:RO_0002422) # Annotation Property: obo:RO_0001900 (temporal interpretation) AnnotationAssertion(obo:IAO_0000115 obo:RO_0001900 "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.") +AnnotationAssertion(rdfs:label obo:RO_0001900 "temporal interpretation") AnnotationAssertion(rdfs:seeAlso obo:RO_0001900 ) SubAnnotationPropertyOf(obo:RO_0001900 obo:RO_0002422) @@ -708,8 +723,8 @@ CONSTRUCT { } WHERE { ?x never_in_taxon: ?taxon . -}"^^xsd:string) -AnnotationAssertion(rdfs:label obo:RO_0002161 "never in taxon"^^xsd:string) +}") +AnnotationAssertion(rdfs:label obo:RO_0002161 "never in taxon") AnnotationAssertion(rdfs:seeAlso obo:RO_0002161 ) SubAnnotationPropertyOf(obo:RO_0002161 obo:RO_0002172) @@ -738,7 +753,7 @@ CONSTRUCT { } WHERE { ?x mutually_spatially_disjoint_with: ?y . -}"^^xsd:string) +}") AnnotationAssertion(rdfs:label obo:RO_0002171 "mutually spatially disjoint with"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0002171 obo:RO_0002163) AnnotationAssertion(rdfs:seeAlso obo:RO_0002171 "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"^^xsd:anyURI) @@ -796,7 +811,7 @@ WHERE { MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label) -}"^^xsd:string) +}") AnnotationAssertion(rdfs:comment obo:RO_0002175 "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.") AnnotationAssertion(rdfs:label obo:RO_0002175 "present in taxon"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0002175 ) @@ -1157,7 +1172,7 @@ SubAnnotationPropertyOf(obo:RO_0040042 obo:RO_0002422) # Annotation Property: obo:valid_for_go_annotation_extension (valid_for_go_annotation_extension) -AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_annotation_extension "pg"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_annotation_extension "pg") AnnotationAssertion(oboInOwl:creation_date obo:valid_for_go_annotation_extension "2020-09-22T11:05:29Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:valid_for_go_annotation_extension "valid_for_go_annotation_extension"@en) AnnotationAssertion(rdfs:seeAlso obo:valid_for_go_annotation_extension ) @@ -1165,7 +1180,7 @@ SubAnnotationPropertyOf(obo:valid_for_go_annotation_extension oboInOwl:SubsetPro # Annotation Property: obo:valid_for_go_gp2term (valid_for_go_gp2term) -AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_gp2term "pg"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_gp2term "pg") AnnotationAssertion(oboInOwl:creation_date obo:valid_for_go_gp2term "2020-09-22T11:05:18Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:valid_for_go_gp2term "valid_for_go_gp2term"@en) AnnotationAssertion(rdfs:seeAlso obo:valid_for_go_gp2term ) @@ -1173,7 +1188,7 @@ SubAnnotationPropertyOf(obo:valid_for_go_gp2term oboInOwl:SubsetProperty) # Annotation Property: obo:valid_for_go_ontology (valid_for_go_ontology) -AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_ontology "pg"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:valid_for_go_ontology "pg") AnnotationAssertion(oboInOwl:creation_date obo:valid_for_go_ontology "2020-09-22T11:04:12Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:valid_for_go_ontology "valid_for_go_ontology"@en) AnnotationAssertion(rdfs:seeAlso obo:valid_for_go_ontology ) @@ -1181,7 +1196,7 @@ SubAnnotationPropertyOf(obo:valid_for_go_ontology oboInOwl:SubsetProperty) # Annotation Property: obo:valid_for_gocam (valid_for_gocam) -AnnotationAssertion(oboInOwl:created_by obo:valid_for_gocam "pg"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:valid_for_gocam "pg") AnnotationAssertion(oboInOwl:creation_date obo:valid_for_gocam "2020-09-22T11:05:45Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:valid_for_gocam "valid_for_gocam"@en) AnnotationAssertion(rdfs:seeAlso obo:valid_for_gocam ) @@ -1195,15 +1210,15 @@ SubAnnotationPropertyOf(subsets:ro-eco oboInOwl:SubsetProperty) # Annotation Property: oboInOwl:SubsetProperty (subset_property) -AnnotationAssertion(rdfs:label oboInOwl:SubsetProperty "subset_property"^^xsd:string) +AnnotationAssertion(rdfs:label oboInOwl:SubsetProperty "subset_property") # Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym) -AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym"^^xsd:string) +AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym") # Annotation Property: oboInOwl:inSubset (in_subset) -AnnotationAssertion(rdfs:label oboInOwl:inSubset "in_subset"^^xsd:string) +AnnotationAssertion(rdfs:label oboInOwl:inSubset "in_subset") ############################ @@ -1373,12 +1388,12 @@ SubObjectPropertyOf(obo:RO_0002002 obo:RO_0002323) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002003 "A relation that holds between two neurons that are electrically coupled via gap junctions.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002003 ) AnnotationAssertion(cito:citesAsAuthority obo:RO_0002003 ) -AnnotationAssertion(rdfs:label obo:RO_0002003 "electrically_synapsed_to"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002003 "electrically_synapsed_to") SubObjectPropertyOf(obo:RO_0002003 obo:RO_0002170) # Object Property: obo:RO_0002004 (tracheates) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002004 "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)."^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002004 "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to).") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002004 ) AnnotationAssertion(rdfs:label obo:RO_0002004 "tracheates"@en) SubObjectPropertyOf(obo:RO_0002004 obo:RO_0001018) @@ -1423,7 +1438,7 @@ ObjectPropertyRange(obo:RO_0002007 obo:BFO_0000040) # Object Property: obo:RO_0002008 (coincident with) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002008 "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other."^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002008 "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.") AnnotationAssertion(obo:IAO_0000116 obo:RO_0002008 "Note from NCEAS meeting: consider changing primary label") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002008 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002008 subsets:ro-eco) @@ -1475,7 +1490,7 @@ ObjectPropertyRange(obo:RO_0002012 obo:BFO_0000003) # Object Property: obo:RO_0002013 (has regulatory component activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002013 "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002013 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002013 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002013 "2017-05-24T09:30:46Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002013 "has regulatory component activity") SubObjectPropertyOf(obo:RO_0002013 obo:RO_0002017) @@ -1484,7 +1499,7 @@ SubObjectPropertyOf(obo:RO_0002013 obo:RO_0002334) # Object Property: obo:RO_0002014 (has negative regulatory component activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002014 "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002014 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002014 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002014 "2017-05-24T09:31:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002014 "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") AnnotationAssertion(rdfs:label obo:RO_0002014 "has negative regulatory component activity") @@ -1494,7 +1509,7 @@ SubObjectPropertyOf(obo:RO_0002014 obo:RO_0002335) # Object Property: obo:RO_0002015 (has positive regulatory component activity) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002015 "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002015 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002015 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002015 "2017-05-24T09:31:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002015 "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") AnnotationAssertion(rdfs:label obo:RO_0002015 "has positive regulatory component activity") @@ -1503,7 +1518,7 @@ SubObjectPropertyOf(obo:RO_0002015 obo:RO_0002336) # Object Property: obo:RO_0002016 (has necessary component activity) -AnnotationAssertion(oboInOwl:created_by obo:RO_0002016 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002016 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002016 "2017-05-24T09:36:08Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002016 "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.") AnnotationAssertion(rdfs:label obo:RO_0002016 "has necessary component activity") @@ -1512,7 +1527,7 @@ SubObjectPropertyOf(obo:RO_0002016 obo:RO_0002336) # Object Property: obo:RO_0002017 (has component activity) -AnnotationAssertion(oboInOwl:created_by obo:RO_0002017 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002017 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002017 "2017-05-24T09:44:33Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002017 "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") AnnotationAssertion(rdfs:label obo:RO_0002017 "has component activity") @@ -1521,7 +1536,7 @@ SubObjectPropertyOf(obo:RO_0002017 obo:RO_0002018) # Object Property: obo:RO_0002018 (has component process) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002018 "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002018 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002018 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002018 "2017-05-24T09:49:21Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002018 "has component process") SubObjectPropertyOf(obo:RO_0002018 obo:RO_0002180) @@ -1531,7 +1546,7 @@ ObjectPropertyRange(obo:RO_0002018 obo:BFO_0000015) # Object Property: obo:RO_0002019 (has ligand) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002019 "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002019 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002019 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002019 "2017-07-19T17:30:36Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002019 "has ligand") SubObjectPropertyOf(obo:RO_0002019 obo:RO_0002233) @@ -1539,7 +1554,7 @@ SubObjectPropertyOf(obo:RO_0002019 obo:RO_0002233) # Object Property: obo:RO_0002020 (transports) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002020 "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002020 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002020 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002020 "2017-07-20T17:11:08Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002020 "transports") SubObjectPropertyOf(obo:RO_0002020 obo:RO_0002313) @@ -1547,24 +1562,24 @@ SubObjectPropertyOf(obo:RO_0002020 obo:RO_0002313) # Object Property: obo:RO_0002021 (occurs across) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002021 "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002021 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002021 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002021 "2017-07-20T17:19:37Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002021 "occurs across") SubObjectPropertyOf(obo:RO_0002021 obo:RO_0002479) # Object Property: obo:RO_0002022 (directly regulated by) -AnnotationAssertion(oboInOwl:created_by obo:RO_0002022 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002022 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002022 "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) rdfs:comment obo:RO_0002022 "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos") rdfs:comment obo:RO_0002022 "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") AnnotationAssertion(rdfs:label obo:RO_0002022 "directly regulated by") SubObjectPropertyOf(obo:RO_0002022 obo:RO_0002334) InverseObjectProperties(obo:RO_0002022 obo:RO_0002578) # Object Property: obo:RO_0002023 (directly negatively regulated by) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) obo:IAO_0000115 obo:RO_0002023 "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002023 "dos"^^xsd:string) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos") obo:IAO_0000115 obo:RO_0002023 "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") +AnnotationAssertion(oboInOwl:created_by obo:RO_0002023 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002023 "2017-09-17T13:52:38Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002023 "directly negatively regulated by") SubObjectPropertyOf(obo:RO_0002023 obo:RO_0002022) @@ -1572,8 +1587,8 @@ InverseObjectProperties(obo:RO_0002023 obo:RO_0002630) # Object Property: obo:RO_0002024 (directly positively regulated by) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) obo:IAO_0000115 obo:RO_0002024 "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002024 "dos"^^xsd:string) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos") obo:IAO_0000115 obo:RO_0002024 "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") +AnnotationAssertion(oboInOwl:created_by obo:RO_0002024 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002024 "2017-09-17T13:52:47Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002024 "directly positively regulated by") SubObjectPropertyOf(obo:RO_0002024 obo:RO_0002022) @@ -1581,8 +1596,8 @@ InverseObjectProperties(obo:RO_0002024 obo:RO_0002629) # Object Property: obo:RO_0002025 (has effector activity) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) obo:IAO_0000115 obo:RO_0002025 "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002025 "dos"^^xsd:string) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos") obo:IAO_0000115 obo:RO_0002025 "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") +AnnotationAssertion(oboInOwl:created_by obo:RO_0002025 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002025 "2017-09-22T14:14:36Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002025 "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") AnnotationAssertion(rdfs:label obo:RO_0002025 "has effector activity") @@ -1591,7 +1606,7 @@ FunctionalObjectProperty(obo:RO_0002025) # Object Property: obo:RO_0002026 (in register with) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) obo:IAO_0000115 obo:RO_0002026 "A relationship that holds between two images, A and B, where: +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:dos") obo:IAO_0000115 obo:RO_0002026 "A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' @@ -1599,7 +1614,7 @@ C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002026 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002026 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002026 "2017-12-07T12:58:06Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002026 "in register with"@en) SubObjectPropertyOf(obo:RO_0002026 obo:RO_0002323) @@ -1682,7 +1697,7 @@ AnnotationAssertion(obo:IAO_0000426 obo:RO_0002101 "(forall (?x ?y) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) - ))))))"^^xsd:string) + ))))))") AnnotationAssertion(obo:RO_0001900 obo:RO_0002101 obo:RO_0001901) AnnotationAssertion(cito:citesAsAuthority obo:RO_0002101 ) AnnotationAssertion(rdfs:label obo:RO_0002101 "fasciculates with"@en) @@ -1726,8 +1741,8 @@ ObjectPropertyRange(obo:RO_0002103 ObjectUnionOf(obo:CL_0000540 ObjectSomeValues AnnotationAssertion(obo:IAO_0000112 obo:RO_0002104 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]"@en) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002104 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002104 "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.") -AnnotationAssertion(obo:IAO_0000117 obo:RO_0002104 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002104 ) +AnnotationAssertion(obo:IAO_0000117 obo:RO_0002104 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002104 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002104 ) AnnotationAssertion(obo:IAO_0000424 obo:RO_0002104 " some ( and some ?Y)") @@ -1970,7 +1985,7 @@ AnnotationAssertion(obo:IAO_0000426 obo:RO_0002132 "(forall (?x ?y) )))))) -"^^xsd:string) +") AnnotationAssertion(obo:RO_0001900 obo:RO_0002132 obo:RO_0001901) AnnotationAssertion(cito:citesAsAuthority obo:RO_0002132 ) AnnotationAssertion(rdfs:label obo:RO_0002132 "has fasciculating neuron projection"@en) @@ -1994,7 +2009,7 @@ ObjectPropertyDomain(obo:RO_0002134 obo:CARO_0001001) # Object Property: obo:RO_0002150 (continuous with) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002150 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002150 "X continuous_with Y if and only if X and Y share a fiat boundary."^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002150 "X continuous_with Y if and only if X and Y share a fiat boundary.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002150 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002150 "connected to") AnnotationAssertion(obo:IAO_0000232 obo:RO_0002150 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)") @@ -2011,14 +2026,14 @@ ObjectPropertyRange(obo:RO_0002150 obo:BFO_0000004) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002151 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002151 "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x") AnnotationAssertion(obo:IAO_0000116 obo:RO_0002151 "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom") -AnnotationAssertion(obo:IAO_0000118 obo:RO_0002151 "proper overlaps"^^xsd:string) +AnnotationAssertion(obo:IAO_0000118 obo:RO_0002151 "proper overlaps") AnnotationAssertion(obo:IAO_0000426 obo:RO_0002151 "(forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) - (not (part_of ?y ?x)))))"^^xsd:string) + (not (part_of ?y ?x)))))") AnnotationAssertion(obo:RO_0001900 obo:RO_0002151 obo:RO_0001901) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002151 subsets:ro-eco) AnnotationAssertion(rdfs:label obo:RO_0002151 "partially overlaps"@en) @@ -2027,10 +2042,10 @@ SubObjectPropertyOf(obo:RO_0002151 obo:RO_0002131) # Object Property: obo:RO_0002156 (derived by descent from) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002156 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002156 "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a."^^xsd:string) -AnnotationAssertion(obo:IAO_0000118 obo:RO_0002156 "ancestral_stucture_of"^^xsd:string) -AnnotationAssertion(obo:IAO_0000118 obo:RO_0002156 "evolutionarily_descended_from"^^xsd:string) -AnnotationAssertion(rdfs:label obo:RO_0002156 "derived by descent from"^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002156 "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.") +AnnotationAssertion(obo:IAO_0000118 obo:RO_0002156 "ancestral_stucture_of") +AnnotationAssertion(obo:IAO_0000118 obo:RO_0002156 "evolutionarily_descended_from") +AnnotationAssertion(rdfs:label obo:RO_0002156 "derived by descent from") SubObjectPropertyOf(obo:RO_0002156 obo:RO_0002320) InverseObjectProperties(obo:RO_0002156 obo:RO_0002157) TransitiveObjectProperty(obo:RO_0002156) @@ -2040,17 +2055,17 @@ TransitiveObjectProperty(obo:RO_0002156) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002157 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002157 "inverse of derived by descent from") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002157 obo:RO_0002259) -AnnotationAssertion(rdfs:label obo:RO_0002157 "has derived by descendant"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002157 "has derived by descendant") SubObjectPropertyOf(obo:RO_0002157 obo:RO_0002320) TransitiveObjectProperty(obo:RO_0002157) # Object Property: obo:RO_0002158 (shares ancestor with) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002158 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002158 "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a."^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002158 "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.") AnnotationAssertion(obo:IAO_0000232 obo:RO_0002158 "Consider obsoleting and merging with child relation, 'in homology relationship with'") -AnnotationAssertion(rdfs:comment obo:RO_0002158 "VBO calls this homologous_to"^^xsd:string) -AnnotationAssertion(rdfs:label obo:RO_0002158 "shares ancestor with"^^xsd:string) +AnnotationAssertion(rdfs:comment obo:RO_0002158 "VBO calls this homologous_to") +AnnotationAssertion(rdfs:label obo:RO_0002158 "shares ancestor with") SubObjectPropertyOf(obo:RO_0002158 obo:RO_0002320) SymmetricObjectProperty(obo:RO_0002158) TransitiveObjectProperty(obo:RO_0002158) @@ -2058,7 +2073,7 @@ TransitiveObjectProperty(obo:RO_0002158) # Object Property: obo:RO_0002159 (serially homologous to) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002159 obo:IAO_0000125) -AnnotationAssertion(rdfs:label obo:RO_0002159 "serially homologous to"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002159 "serially homologous to") SubObjectPropertyOf(obo:RO_0002159 obo:RO_0002320) SymmetricObjectProperty(obo:RO_0002159) TransitiveObjectProperty(obo:RO_0002159) @@ -2074,7 +2089,7 @@ AnnotationAssertion(obo:IAO_0000116 obo:RO_0002160 "The original intent was to t AnnotationAssertion(obo:IAO_0000117 obo:RO_0002160 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002160 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002160 ) -AnnotationAssertion(rdfs:label obo:RO_0002160 "only in taxon"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002160 "only in taxon") AnnotationAssertion(rdfs:seeAlso obo:RO_0002160 ) SubObjectPropertyOf(obo:RO_0002160 obo:RO_0002162) @@ -2082,13 +2097,13 @@ SubObjectPropertyOf(obo:RO_0002160 obo:RO_0002162) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002162 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002162 "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.") -AnnotationAssertion(obo:IAO_0000117 obo:RO_0002162 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002162 ) +AnnotationAssertion(obo:IAO_0000117 obo:RO_0002162 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002162 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002162 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002162 subsets:ro-eco) -AnnotationAssertion(rdfs:comment obo:RO_0002162 "Connects a biological entity to its taxon of origin."^^xsd:string) -AnnotationAssertion(rdfs:label obo:RO_0002162 "in taxon"^^xsd:string) +AnnotationAssertion(rdfs:comment obo:RO_0002162 "Connects a biological entity to its taxon of origin.") +AnnotationAssertion(rdfs:label obo:RO_0002162 "in taxon") AnnotationAssertion(rdfs:seeAlso obo:RO_0002162 ) SubObjectPropertyOf(obo:RO_0002162 obo:RO_0002320) ObjectPropertyRange(obo:RO_0002162 obo:CARO_0001010) @@ -2104,7 +2119,7 @@ AnnotationAssertion(obo:IAO_0000232 obo:RO_0002163 "Note that it would be possib AnnotationAssertion(obo:IAO_0000424 obo:RO_0002163 "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)") AnnotationAssertion(obo:RO_0001900 obo:RO_0002163 obo:RO_0001901) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002163 subsets:ro-eco) -AnnotationAssertion(rdfs:label obo:RO_0002163 "spatially disjoint from"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002163 "spatially disjoint from") AnnotationAssertion(rdfs:seeAlso obo:RO_0002163 "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern"^^xsd:anyURI) SubObjectPropertyOf(obo:RO_0002163 obo:RO_0002323) @@ -2197,9 +2212,9 @@ FunctionalObjectProperty(obo:RO_0002201) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002202 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002202 "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y") +AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 ) -AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 ) AnnotationAssertion(rdfs:comment obo:RO_0002202 "This is the transitive form of the develops from relation") AnnotationAssertion(rdfs:label obo:RO_0002202 "develops from"@en) @@ -2304,9 +2319,9 @@ SubObjectPropertyOf(obo:RO_0002210 obo:RO_0002203) # Object Property: obo:RO_0002211 (regulates) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002211 "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") -AnnotationAssertion(obo:IAO_0000117 obo:RO_0002211 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002211 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002211 ) +AnnotationAssertion(obo:IAO_0000117 obo:RO_0002211 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002211 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002211 "GO") AnnotationAssertion(obo:IAO_0000232 obo:RO_0002211 "Regulation precludes parthood; the regulatory process may not be within the regulated process.") @@ -2398,8 +2413,8 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002217 "OBSOLETE x actively particip AnnotationAssertion(obo:IAO_0000117 obo:RO_0002217 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002217 "agent in") AnnotationAssertion(obo:IAO_0100001 obo:RO_0002217 obo:RO_0002608) -AnnotationAssertion(rdfs:comment obo:RO_0002217 "Obsoleted as the inverse property was obsoleted."^^xsd:string) -AnnotationAssertion(rdfs:label obo:RO_0002217 "obsolete actively participates in"^^xsd:string) +AnnotationAssertion(rdfs:comment obo:RO_0002217 "Obsoleted as the inverse property was obsoleted.") +AnnotationAssertion(rdfs:label obo:RO_0002217 "obsolete actively participates in") AnnotationAssertion(owl:deprecated obo:RO_0002217 "true"^^xsd:boolean) # Object Property: obo:RO_0002218 (obsolete has active participant) @@ -2408,7 +2423,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0002218 "OBSOLETE x has participant y AnnotationAssertion(obo:IAO_0000117 obo:RO_0002218 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002218 "has agent") AnnotationAssertion(obo:IAO_0100001 obo:RO_0002218 obo:RO_0002500) -AnnotationAssertion(rdfs:label obo:RO_0002218 "obsolete has active participant"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002218 "obsolete has active participant") AnnotationAssertion(owl:deprecated obo:RO_0002218 "true"^^xsd:boolean) # Object Property: obo:RO_0002219 (surrounded by) @@ -2705,9 +2720,9 @@ SubObjectPropertyOf(obo:RO_0002255 obo:RO_0002385) AnnotationAssertion(obo:IAO_0000114 obo:RO_0002256 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002256 "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T") +AnnotationAssertion(obo:IAO_0000117 obo:RO_0002256 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002256 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002256 ) -AnnotationAssertion(obo:IAO_0000117 obo:RO_0002256 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002256 "induced by") AnnotationAssertion(obo:IAO_0000119 obo:RO_0002256 ) AnnotationAssertion(obo:IAO_0000119 obo:RO_0002256 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)") @@ -2742,6 +2757,24 @@ InverseObjectProperties(obo:RO_0002258 obo:RO_0002286) ObjectPropertyDomain(obo:RO_0002258 obo:BFO_0000002) ObjectPropertyRange(obo:RO_0002258 obo:BFO_0000002) +# Object Property: obo:RO_0002260 (has biological role) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002260 "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)") +AnnotationAssertion(rdfs:label obo:RO_0002260 "has biological role") +SubObjectPropertyOf(obo:RO_0002260 obo:RO_0000087) + +# Object Property: obo:RO_0002261 (has application role) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002261 "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)") +AnnotationAssertion(rdfs:label obo:RO_0002261 "has application role") +SubObjectPropertyOf(obo:RO_0002261 obo:RO_0000087) + +# Object Property: obo:RO_0002262 (has chemical role) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002262 "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)") +AnnotationAssertion(rdfs:label obo:RO_0002262 "has chemical role") +SubObjectPropertyOf(obo:RO_0002262 obo:RO_0000087) + # Object Property: obo:RO_0002263 (acts upstream of) AnnotationAssertion(obo:IAO_0000112 obo:RO_0002263 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") @@ -2954,9 +2987,9 @@ SubObjectPropertyOf(obo:RO_0002305 obo:RO_0004046) # Object Property: obo:RO_0002309 (has exposure stimulus) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002309 "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.") +AnnotationAssertion(dc:contributor obo:RO_0002309 ) AnnotationAssertion(dc:contributor obo:RO_0002309 ) AnnotationAssertion(dc:contributor obo:RO_0002309 ) -AnnotationAssertion(dc:contributor obo:RO_0002309 ) AnnotationAssertion(oboInOwl:created_by obo:RO_0002309 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0002309 "2017-06-05T17:35:04Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0002309 "has exposure stimulus") @@ -3252,7 +3285,7 @@ SubObjectPropertyOf(obo:RO_0002344 obo:RO_0002337) # Object Property: obo:RO_0002345 (exports) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002345 "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s."^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002345 "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002345 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0002345 obo:valid_for_go_ontology) AnnotationAssertion(rdfs:label obo:RO_0002345 "exports"@en) @@ -3560,7 +3593,7 @@ AnnotationAssertion(obo:IAO_0000114 obo:RO_0002401 obo:IAO_0000428) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002401 ) AnnotationAssertion(rdfs:comment obo:RO_0002401 "Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit") -AnnotationAssertion(rdfs:label obo:RO_0002401 "obsolete has indirect input"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002401 "obsolete has indirect input") AnnotationAssertion(owl:deprecated obo:RO_0002401 "true"^^xsd:boolean) # Object Property: obo:RO_0002402 (obsolete has direct output) @@ -3570,7 +3603,7 @@ AnnotationAssertion(obo:IAO_0000114 obo:RO_0002402 obo:IAO_0000428) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002402 "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. ") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002402 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002402 "directly produces") -AnnotationAssertion(rdfs:label obo:RO_0002402 "obsolete has direct output"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002402 "obsolete has direct output") AnnotationAssertion(owl:deprecated obo:RO_0002402 "true"^^xsd:boolean) # Object Property: obo:RO_0002403 (obsolete has indirect output) @@ -3579,7 +3612,7 @@ AnnotationAssertion(obo:IAO_0000114 obo:RO_0002403 obo:IAO_0000428) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002403 ) AnnotationAssertion(rdfs:comment obo:RO_0002403 "Likely to be obsoleted. See: https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit") -AnnotationAssertion(rdfs:label obo:RO_0002403 "obsolete has indirect output"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002403 "obsolete has indirect output") AnnotationAssertion(owl:deprecated obo:RO_0002403 "true"^^xsd:boolean) # Object Property: obo:RO_0002404 (causally downstream of) @@ -3604,7 +3637,7 @@ InverseObjectProperties(obo:RO_0002405 obo:RO_0002412) # Object Property: obo:RO_0002406 (obsolete directly activates) AnnotationAssertion(obo:IAO_0100001 obo:RO_0002406 obo:RO_0002629) -AnnotationAssertion(rdfs:comment obo:RO_0002406 "This term was obsoleted because it has the same meaning as 'directly positively regulates'."^^xsd:string) +AnnotationAssertion(rdfs:comment obo:RO_0002406 "This term was obsoleted because it has the same meaning as 'directly positively regulates'.") AnnotationAssertion(rdfs:label obo:RO_0002406 "obsolete directly activates"@en) AnnotationAssertion(owl:deprecated obo:RO_0002406 "true"^^xsd:boolean) @@ -3622,7 +3655,7 @@ TransitiveObjectProperty(obo:RO_0002407) # Object Property: obo:RO_0002408 (obsolete directly inhibits) AnnotationAssertion(obo:IAO_0100001 obo:RO_0002408 obo:RO_0002630) -AnnotationAssertion(rdfs:comment obo:RO_0002408 "This term was obsoleted because it has the same meaning as 'directly negatively regulates'."^^xsd:string) +AnnotationAssertion(rdfs:comment obo:RO_0002408 "This term was obsoleted because it has the same meaning as 'directly negatively regulates'.") AnnotationAssertion(rdfs:label obo:RO_0002408 "obsolete directly inhibits"@en) AnnotationAssertion(owl:deprecated obo:RO_0002408 "true"^^xsd:boolean) @@ -3786,7 +3819,7 @@ SubObjectPropertyOf(obo:RO_0002431 obo:RO_0002500) # Object Property: obo:RO_0002432 (is active in) AnnotationAssertion(obo:IAO_0000112 obo:RO_0002432 "A protein that enables activity in a cytosol.") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cjm"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:dos"^^xsd:string) obo:IAO_0000115 obo:RO_0002432 "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cjm") Annotation(oboInOwl:hasDbXref "GOC:dos") obo:IAO_0000115 obo:RO_0002432 "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002432 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002432 "executes activity in") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002432 "enables activity in") @@ -3805,8 +3838,8 @@ SubObjectPropertyOf(obo:RO_0002433 obo:RO_0002131) # Object Property: obo:RO_0002434 (interacts with) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002434 "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") +AnnotationAssertion(obo:IAO_0000116 obo:RO_0002434 "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002434 ) AnnotationAssertion(obo:IAO_0000232 obo:RO_0002434 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002434 "in pairwise interaction with") @@ -3869,9 +3902,9 @@ SubObjectPropertyOf(obo:RO_0002438 obo:RO_0002574) AnnotationAssertion(obo:IAO_0000112 obo:RO_0002439 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]") AnnotationAssertion(obo:IAO_0000112 obo:RO_0002439 "Baleen whale preys on krill") AnnotationAssertion(obo:IAO_0000115 obo:RO_0002439 "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members") +AnnotationAssertion(obo:IAO_0000117 obo:RO_0002439 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002439 ) AnnotationAssertion(obo:IAO_0000117 obo:RO_0002439 ) -AnnotationAssertion(obo:IAO_0000117 obo:RO_0002439 ) AnnotationAssertion(obo:IAO_0000118 obo:RO_0002439 "is subject of predation interaction with") AnnotationAssertion(obo:IAO_0000118 obo:RO_0002439 "preys upon") AnnotationAssertion(oboInOwl:inSubset obo:RO_0002439 subsets:ro-eco) @@ -4299,9 +4332,9 @@ SubObjectPropertyOf(obo:RO_0002490 obo:RO_0002487) # Object Property: obo:RO_0002491 (existence starts and ends during) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0002491 "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)"^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0002491 "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)") AnnotationAssertion(obo:IAO_0000117 obo:RO_0002491 ) -AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002491 "exists during"^^xsd:string) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:RO_0002491 "exists during") AnnotationAssertion(rdfs:comment obo:RO_0002491 "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.") AnnotationAssertion(rdfs:label obo:RO_0002491 "existence starts and ends during") SubObjectPropertyOf(obo:RO_0002491 obo:RO_0002488) @@ -5083,7 +5116,7 @@ SubObjectPropertyOf(obo:RO_0002608 obo:RO_0002410) AnnotationAssertion(obo:IAO_0000115 obo:RO_0002609 "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.") AnnotationAssertion(obo:IAO_0000232 obo:RO_0002609 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label obo:RO_0002609 "obsolete related via dependence to"^^xsd:string) +AnnotationAssertion(rdfs:label obo:RO_0002609 "obsolete related via dependence to") AnnotationAssertion(owl:deprecated obo:RO_0002609 "true"^^xsd:boolean) # Object Property: obo:RO_0002610 (correlated with) @@ -5269,10 +5302,10 @@ SymmetricObjectProperty(obo:RO_0002801) # Object Property: obo:RO_0003000 (produces) AnnotationAssertion(obo:IAO_0000114 obo:RO_0003000 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0003000 "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix."^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0003000 "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.") AnnotationAssertion(obo:IAO_0000117 obo:RO_0003000 ) AnnotationAssertion(oboInOwl:inSubset obo:RO_0003000 subsets:ro-eco) -AnnotationAssertion(rdfs:comment obo:RO_0003000 "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue."^^xsd:string) +AnnotationAssertion(rdfs:comment obo:RO_0003000 "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.") AnnotationAssertion(rdfs:label obo:RO_0003000 "produces"@en) InverseObjectProperties(obo:RO_0003000 obo:RO_0003001) ObjectPropertyDomain(obo:RO_0003000 obo:BFO_0000040) @@ -5463,7 +5496,7 @@ SubObjectPropertyOf(obo:RO_0004007 obo:RO_0000057) # Object Property: obo:RO_0004008 (has primary output) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cjm"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:dph"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:kva") Annotation(oboInOwl:hasDbXref "GOC:pt") Annotation(rdfs:comment "PMID:27812932") obo:IAO_0000115 obo:RO_0004008 "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:kva") Annotation(oboInOwl:hasDbXref "GOC:pt") Annotation(oboInOwl:hasDbXref "GOC:cjm") Annotation(oboInOwl:hasDbXref "GOC:dph") Annotation(rdfs:comment "PMID:27812932") obo:IAO_0000115 obo:RO_0004008 "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.") AnnotationAssertion(oboInOwl:created_by obo:RO_0004008 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0004008 "2018-12-13T11:26:32Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0004008 obo:valid_for_go_ontology) @@ -5473,7 +5506,7 @@ SubObjectPropertyOf(obo:RO_0004008 obo:RO_0004007) # Object Property: obo:RO_0004009 (has primary input) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:cjm"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:dph"^^xsd:string) Annotation(oboInOwl:hasDbXref "GOC:kva") Annotation(oboInOwl:hasDbXref "GOC:pt") Annotation(rdfs:comment "PMID:27812932") obo:IAO_0000115 obo:RO_0004009 "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:kva") Annotation(oboInOwl:hasDbXref "GOC:pt") Annotation(oboInOwl:hasDbXref "GOC:cjm") Annotation(oboInOwl:hasDbXref "GOC:dph") Annotation(rdfs:comment "PMID:27812932") obo:IAO_0000115 obo:RO_0004009 "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.") AnnotationAssertion(oboInOwl:created_by obo:RO_0004009 ) AnnotationAssertion(oboInOwl:creation_date obo:RO_0004009 "2018-12-13T11:26:56Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0004009 obo:valid_for_go_ontology) @@ -5888,10 +5921,10 @@ AnnotationAssertion(obo:IAO_0000112 obo:RO_0009501 "A drought sensitivity trait AnnotationAssertion(obo:IAO_0000112 obo:RO_0009501 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)") AnnotationAssertion(obo:IAO_0000112 obo:RO_0009501 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.") AnnotationAssertion(obo:IAO_0000115 obo:RO_0009501 "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.") +AnnotationAssertion(dc:contributor obo:RO_0009501 ) AnnotationAssertion(dc:contributor obo:RO_0009501 ) AnnotationAssertion(dc:contributor obo:RO_0009501 ) AnnotationAssertion(dc:contributor obo:RO_0009501 ) -AnnotationAssertion(dc:contributor obo:RO_0009501 ) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "RO:cjm") oboInOwl:hasExactSynonym obo:RO_0009501 "triggered by process") AnnotationAssertion(rdfs:label obo:RO_0009501 "realized in response to"@en) AnnotationAssertion(rdfs:seeAlso obo:RO_0009501 "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"^^xsd:anyURI) @@ -6060,8 +6093,8 @@ SubObjectPropertyOf(obo:RO_0011024 obo:RO_0011022) # Object Property: obo:RO_0012000 (has small molecule regulator) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012000 "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant"^^xsd:string) -AnnotationAssertion(oboInOwl:created_by obo:RO_0012000 "pg"^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012000 "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant") +AnnotationAssertion(oboInOwl:created_by obo:RO_0012000 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012000 "2020-04-22T20:27:26Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012000 "has small molecule regulator"@en) SubObjectPropertyOf(obo:RO_0012000 obo:RO_0000057) @@ -6069,8 +6102,8 @@ InverseObjectProperties(obo:RO_0012000 obo:RO_0012004) # Object Property: obo:RO_0012001 (has small molecule activator) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012001 "a relation between a process and a continuant, in which the process is activated by the small molecule continuant"^^xsd:string) -AnnotationAssertion(oboInOwl:created_by obo:RO_0012001 "pg"^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012001 "a relation between a process and a continuant, in which the process is activated by the small molecule continuant") +AnnotationAssertion(oboInOwl:created_by obo:RO_0012001 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012001 "2020-04-22T20:28:37Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012001 "has small molecule activator"@en) SubObjectPropertyOf(obo:RO_0012001 obo:RO_0012000) @@ -6078,8 +6111,8 @@ InverseObjectProperties(obo:RO_0012001 obo:RO_0012005) # Object Property: obo:RO_0012002 (has small molecule inhibitor) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012002 "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant"^^xsd:string) -AnnotationAssertion(oboInOwl:created_by obo:RO_0012002 "pg"^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012002 "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant") +AnnotationAssertion(oboInOwl:created_by obo:RO_0012002 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012002 "2020-04-22T20:28:54Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012002 "has small molecule inhibitor"@en) SubObjectPropertyOf(obo:RO_0012002 obo:RO_0012000) @@ -6087,8 +6120,8 @@ InverseObjectProperties(obo:RO_0012002 obo:RO_0012006) # Object Property: obo:RO_0012003 (acts on population of) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012003 "p acts on population of c iff c' is a collection, has members of type c, and p has participant c"^^xsd:string) -AnnotationAssertion(oboInOwl:created_by obo:RO_0012003 "pg"^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012003 "p acts on population of c iff c' is a collection, has members of type c, and p has participant c") +AnnotationAssertion(oboInOwl:created_by obo:RO_0012003 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012003 "2020-06-08T17:21:33Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012003 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012003 obo:valid_for_go_ontology) @@ -6098,16 +6131,16 @@ SubObjectPropertyOf(obo:RO_0012003 obo:RO_0000057) # Object Property: obo:RO_0012004 (is small molecule regulator of) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012004 "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process"^^xsd:string) -AnnotationAssertion(oboInOwl:created_by obo:RO_0012004 "pg"^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012004 "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process") +AnnotationAssertion(oboInOwl:created_by obo:RO_0012004 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012004 "2020-06-24T13:15:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012004 "is small molecule regulator of"@en) SubObjectPropertyOf(obo:RO_0012004 obo:RO_0002596) # Object Property: obo:RO_0012005 (is small molecule activator of) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012005 "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process"^^xsd:string) -AnnotationAssertion(oboInOwl:created_by obo:RO_0012005 "pg"^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012005 "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process") +AnnotationAssertion(oboInOwl:created_by obo:RO_0012005 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012005 "2020-06-24T13:15:26Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012005 "is small molecule activator of"@en) SubObjectPropertyOf(obo:RO_0012005 obo:RO_0002598) @@ -6115,8 +6148,8 @@ SubObjectPropertyOf(obo:RO_0012005 obo:RO_0012004) # Object Property: obo:RO_0012006 (is small molecule inhibitor of) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012006 "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process"^^xsd:string) -AnnotationAssertion(oboInOwl:created_by obo:RO_0012006 "pg"^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012006 "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process") +AnnotationAssertion(oboInOwl:created_by obo:RO_0012006 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012006 "2020-06-24T13:15:35Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012006 "is small molecule inhibitor of"@en) SubObjectPropertyOf(obo:RO_0012006 obo:RO_0002597) @@ -6124,15 +6157,15 @@ SubObjectPropertyOf(obo:RO_0012006 obo:RO_0012004) # Object Property: obo:RO_0012007 (results in adhesion of) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0012007 "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities."^^xsd:string) -AnnotationAssertion(oboInOwl:created_by obo:RO_0012007 "pg"^^xsd:string) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0012007 "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities.") +AnnotationAssertion(oboInOwl:created_by obo:RO_0012007 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012007 "2020-08-27T08:13:59Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012007 "results in adhesion of"@en) SubObjectPropertyOf(obo:RO_0012007 obo:RO_0040036) # Object Property: obo:RO_0012008 (results in fusion of) -AnnotationAssertion(oboInOwl:created_by obo:RO_0012008 "pg"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012008 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012008 "2021-02-26T07:28:29Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012008 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012008 obo:valid_for_go_ontology) @@ -6143,7 +6176,7 @@ SubObjectPropertyOf(obo:RO_0012008 obo:RO_0002592) # Object Property: obo:RO_0012009 (constitutively upstream of) AnnotationAssertion(obo:IAO_0000115 obo:RO_0012009 "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012009 "pg"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012009 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012009 "2022-09-26T06:01:01Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012009 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012009 obo:valid_for_gocam) @@ -6153,7 +6186,7 @@ SubObjectPropertyOf(obo:RO_0012009 obo:RO_0002304) # Object Property: obo:RO_0012010 (removes input for) AnnotationAssertion(obo:IAO_0000115 obo:RO_0012010 "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012010 "pg"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012010 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012010 "2022-09-26T06:06:20Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012010 obo:valid_for_go_annotation_extension) AnnotationAssertion(oboInOwl:inSubset obo:RO_0012010 obo:valid_for_gocam) @@ -6163,7 +6196,7 @@ SubObjectPropertyOf(obo:RO_0012010 obo:RO_0002305) # Object Property: obo:RO_0012011 (indirectly causally upstream of) AnnotationAssertion(obo:IAO_0000115 obo:RO_0012011 "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012011 "pg"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012011 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012011 "2022-09-26T06:07:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012011 "indirectly causally upstream of"@en) SubObjectPropertyOf(obo:RO_0012011 obo:RO_0002411) @@ -6171,7 +6204,7 @@ SubObjectPropertyOf(obo:RO_0012011 obo:RO_0002411) # Object Property: obo:RO_0012012 (indirectly regulates) AnnotationAssertion(obo:IAO_0000115 obo:RO_0012012 "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0012012 "pg"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0012012 "pg") AnnotationAssertion(oboInOwl:creation_date obo:RO_0012012 "2022-09-26T06:08:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:RO_0012012 "indirectly regulates"@en) SubObjectPropertyOf(obo:RO_0012012 obo:RO_0002211) @@ -6317,7 +6350,7 @@ ObjectPropertyRange(obo:RO_0015006 obo:PATO_0000001) # Object Property: obo:RO_0015007 (increased in magnitude relative to) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0002-6601-2165") obo:IAO_0000115 obo:RO_0015007 "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.") -AnnotationAssertion(rdfs:comment obo:RO_0015007 "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'."^^xsd:string) +AnnotationAssertion(rdfs:comment obo:RO_0015007 "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.") AnnotationAssertion(rdfs:label obo:RO_0015007 "increased in magnitude relative to") SubObjectPropertyOf(obo:RO_0015007 obo:RO_0015006) ObjectPropertyDomain(obo:RO_0015007 obo:PATO_0000001) @@ -6326,7 +6359,7 @@ ObjectPropertyRange(obo:RO_0015007 obo:PATO_0000001) # Object Property: obo:RO_0015008 (decreased in magnitude relative to) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0002-6601-2165") obo:IAO_0000115 obo:RO_0015008 "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.") -AnnotationAssertion(rdfs:comment obo:RO_0015008 "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'."^^xsd:string) +AnnotationAssertion(rdfs:comment obo:RO_0015008 "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.") AnnotationAssertion(rdfs:label obo:RO_0015008 "decreased in magnitude relative to") SubObjectPropertyOf(obo:RO_0015008 obo:RO_0015006) ObjectPropertyDomain(obo:RO_0015008 obo:PATO_0000001) @@ -6344,13 +6377,13 @@ AnnotationAssertion(rdfs:label obo:RO_0015010 "has relative magnitude") # Object Property: obo:RO_0015011 (has cross section) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0002-6601-2165") obo:IAO_0000115 obo:RO_0015011 "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.") -AnnotationAssertion(rdfs:comment obo:RO_0015011 "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round."^^xsd:string) +AnnotationAssertion(rdfs:comment obo:RO_0015011 "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.") AnnotationAssertion(rdfs:label obo:RO_0015011 "has cross section") # Object Property: obo:RO_0015012 (reciprocal of) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0002-6601-2165") obo:IAO_0000115 obo:RO_0015012 "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.") -AnnotationAssertion(rdfs:comment obo:RO_0015012 "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality."^^xsd:string) +AnnotationAssertion(rdfs:comment obo:RO_0015012 "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.") AnnotationAssertion(rdfs:label obo:RO_0015012 "reciprocal of") # Object Property: obo:RO_0015015 (has high plasma membrane amount) @@ -6528,7 +6561,7 @@ SubObjectPropertyOf(obo:RO_HOM0000003 obo:RO_0002320) # Data Property: obo:RO_0002029 (has increased age-specific mortality rate) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24138933") Annotation(oboInOwl:hasDbXref "Wikipedia:Infant_mortality") obo:IAO_0000115 obo:RO_0002029 "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.") -AnnotationAssertion(oboInOwl:created_by obo:RO_0002029 "dos"^^xsd:string) +AnnotationAssertion(oboInOwl:created_by obo:RO_0002029 "dos") AnnotationAssertion(oboInOwl:creation_date obo:RO_0002029 "2018-05-22T16:43:28Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment obo:RO_0002029 "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses.") AnnotationAssertion(rdfs:label obo:RO_0002029 "has increased age-specific mortality rate"@en) @@ -6557,7 +6590,7 @@ SubClassOf(obo:BFO_0000015 ObjectAllValuesFrom(obo:RO_0002214 obo:BFO_0000015)) SubClassOf(obo:CHEBI_50906 obo:PATO_0000001) -# Class: obo:GO_0004842 (ubiquitin-protein ligase activity) +# Class: obo:GO_0004842 (ubiquitin-protein transferase activity) SubClassOf(obo:GO_0004842 ObjectHasSelf(obo:RO_0002482)) @@ -6565,7 +6598,7 @@ SubClassOf(obo:GO_0004842 ObjectHasSelf(obo:RO_0002482)) SubClassOf(obo:GO_0016301 ObjectHasSelf(obo:RO_0002481)) -# Class: obo:GO_0019107 (obo:GO_0019107) +# Class: obo:GO_0019107 (myristoyltransferase activity) SubClassOf(obo:GO_0019107 ObjectHasSelf(obo:RO_0018001)) @@ -6615,6 +6648,63 @@ AnnotationAssertion(rdfs:label obo:RO_0002577 "system") SubClassOf(obo:RO_0002577 obo:BFO_0000040) +############################ +# Named Individuals +############################ + +# Individual: obo:RO_0001901 (axiom holds for all times) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0001901 "## Elucidation + +This is used when the statement/axiom is assumed to hold true 'eternally' + +## How to interpret (informal) + +First the "atemporal" FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation") +AnnotationAssertion(rdfs:label obo:RO_0001901 "axiom holds for all times"@en) + +# Individual: obo:RO_0001902 (relation has no temporal argument) + +AnnotationAssertion(obo:IAO_0000115 obo:RO_0001902 "## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y)") +AnnotationAssertion(rdfs:label obo:RO_0001902 "relation has no temporal argument"@en) + + SubClassOf(ObjectSomeValuesFrom(obo:RO_0002566 obo:BFO_0000040) ObjectUnionOf(ObjectSomeValuesFrom(obo:RO_0000056 ObjectSomeValuesFrom(obo:RO_0002418 obo:BFO_0000015)) ObjectSomeValuesFrom(obo:RO_0002215 ObjectSomeValuesFrom(obo:RO_0000056 ObjectSomeValuesFrom(obo:RO_0002418 obo:BFO_0000015))))) SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000050 obo:BFO_0000050) obo:RO_0002131) SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000050 obo:BFO_0000062) obo:BFO_0000062) @@ -6760,27 +6850,27 @@ SubObjectPropertyOf(ObjectPropertyChain(obo:RO_0015001 obo:RO_0015003) obo:RO_00 SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf(obo:BFO_0000066) obo:RO_0002234) obo:RO_0003000) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf(obo:RO_0002176) obo:RO_0002176) obo:RO_0002170) DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002180 Variable() Variable()) ClassAtom(obo:BFO_0000015 Variable()) ClassAtom(obo:BFO_0000015 Variable()))Head(ObjectPropertyAtom(obo:RO_0002018 Variable() Variable()))) -DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z"^^xsd:string) Annotation(rdfs:label "infer input from direct reg"^^xsd:string) Body(ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()) ClassAtom(obo:GO_0003674 Variable()) ClassAtom(obo:GO_0003674 Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) +DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()) ClassAtom(obo:GO_0003674 Variable()) ClassAtom(obo:GO_0003674 Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom(obo:GO_0003674 Variable()) ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()) ObjectPropertyAtom(obo:BFO_0000051 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()))) -DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'"^^xsd:string) Annotation(rdfs:label "involved in BP"^^xsd:string) Body(ClassAtom(obo:GO_0008150 Variable()) ObjectPropertyAtom(obo:BFO_0000050 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002331 Variable() Variable()))) +DLSafeRule(Annotation(swrla:isRuleEnabled "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom(obo:GO_0008150 Variable()) ObjectPropertyAtom(obo:BFO_0000050 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002327 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002331 Variable() Variable()))) DLSafeRule(Annotation(rdfs:seeAlso ) Body(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()) ClassAtom(obo:GO_0016301 Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002447 Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002013 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002014 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom(obo:RO_0002352 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002333 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002015 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002404 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002211 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012012 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0019002 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0019001 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002264 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002263 Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002233 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002578 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002629 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002025 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002630 Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002404 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom(obo:RO_0002131 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002211 Variable() Variable()) ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012012 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002213 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002212 Variable() Variable()) ObjectPropertyAtom(obo:RO_0019002 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0019001 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002264 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0002263 Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()) ObjectPropertyAtom(obo:RO_0002411 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0012011 Variable() Variable()))) AnnotationAssertion(owl:deprecated obo:BFO_0000060 "true"^^xsd:boolean) AnnotationAssertion(obo:IAO_0000115 obo:RO_0000092 "inverse of has disposition") AnnotationAssertion(oboInOwl:inSubset obo:RO_0000092 obo:RO_0002259) diff --git a/src/ontology/ro-odk.yaml b/src/ontology/ro-odk.yaml new file mode 100644 index 00000000..d3815d4b --- /dev/null +++ b/src/ontology/ro-odk.yaml @@ -0,0 +1,73 @@ +id: ro +title: "OBO Relations Ontology" +github_org: oborel +repo: obo-relations +report_fail_on: Error +edit_format: owl +export_formats: + - owl + - obo + - json +release_artefacts: + - base + - full + - custom-core +primary_release: full +namespaces: + - http://purl.obolibrary.org/obo/RO_ + - http://purl.obolibrary.org/obo/BFO_0000050 + - http://purl.obolibrary.org/obo/BFO_0000051 + - http://purl.obolibrary.org/obo/BFO_0000060 +import_group: + products: + - id: omo + module_type: filter + - id: pato + make_base: TRUE + module_type: minimal + - id: cl + make_base: TRUE + module_type: minimal + - id: envo + make_base: TRUE + module_type: minimal + - id: go + make_base: TRUE + module_type: minimal + - id: caro + make_base: TRUE + module_type: minimal + - id: other + module_type: custom + mirror_type: no_mirror +subset_group: + products: + - id: ro-interaction + - id: ro-sequence + - id: ro-time-interval + - id: ro-mereotopology + - id: ro-causal + - id: ro-developmental + - id: ro-eco + - id: ro-hom + - id: ro-chado + - id: ro-biotic-interaction +components: + products: + - filename: core.owl + - filename: el-constraints.owl + - filename: generated-axioms.owl + - filename: temporal-intervals.owl + - filename: bfo-axioms.owl + - filename: bfo-classes-minimal.owl + - filename: rohom.owl +robot_java_args: '-Xmx8G' +robot_report: + release_reports: False + fail_on: ERROR + use_labels: False + custom_profile: True + use_base_iris: True + report_on: + - edit + - ro-base.owl diff --git a/src/ontology/ro.Makefile b/src/ontology/ro.Makefile new file mode 100644 index 00000000..88dceb8e --- /dev/null +++ b/src/ontology/ro.Makefile @@ -0,0 +1,185 @@ +## Customize Makefile settings for ro +## +## If you need to customize your Makefile, make +## changes here rather than in the main Makefile + +# ======================================== +# PRODUCTION +# ======================================== + +# fairly dump release process whilst waiting for Oort - check than versionIRI has been entered manually. +#ro.owl: ro-edit.owl components/core.owl components/temporal-intervals.owl validate-using-oort +# $(OWLTOOLS) --use-catalog $< --set-ontology-id -v $(URIBASE)/ro/releases/$(RELEASEDATE)/ro.owl $(URI)/ro.owl -o file://`pwd`/$@ +# grep versionIRI $< && (echo "check the version:" && echo versionIRI: `grep versionIRI $<` && cp $< $@) || echo 'You must set the versionIRI!!' + +#%-sh.obo: %.owl +# $(OWLTOOLS) --use-catalog $< --merge-import-closure --add-obo-shorthand-to-properties -o -f obo $@.tmp && grep -v ^owl-axioms $@.tmp > $@ + +# soon this will be incorporated into Oort +#ro-el.owl: ro.owl +# makeElWithoutReasoning.sh -i `pwd`/$< -o `pwd`/$@ + +# note we don't do anything with the generated ontology, this is just for checking purposes. +validate-using-oort: ro-edit.owl + ontology-release-runner --catalog-xml catalog-v001.xml --outdir build --simple --allow-overwrite --reasoner hermit ro-edit.owl + touch $@ + +# ======================================== +# Custom components +# ======================================== + +core.owl: components/core.owl components/bfo-axioms.owl components/bfo-classes-minimal.owl + $(ROBOT) merge -i components/core.owl -i components/bfo-axioms.owl -i components/bfo-classes-minimal.owl annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@ + +# ======================================== +# Custom imports +# ======================================== + +$(IMPORTDIR)/other_import.owl: + echo "$@ is manually maintained." && touch $@ + +# ======================================== +# DOCUMENTATION +# ======================================== +# requires mkdocs: `pip install mkdocs` +docs-serve: + (cd ../.. && mkdocs serve) +docs-deploy: + (cd ../.. && mkdocs gh-deploy) + + +# ======================================== +# DIFFS +# ======================================== +ro-lastbuild.owl: ro-edit.owl + $(ROBOT) merge -I $(URIBASE)/ro.owl -o $@ + +ro-lastbuild-core.owl: ro-edit.owl + $(ROBOT) merge -I $(URIBASE)/ro/core.owl -o $@ + +ro-diff.txt: ro.owl ro-lastbuild.owl + $(ROBOT) diff --left ro-lastbuild.owl --right ro.owl -o $@ + +ro-diff-core.txt: core.owl ro-lastbuild-core.owl + $(ROBOT) diff --left ro-lastbuild-core.owl --right core.owl -o $@ + +dev-diffs: + $(MAKE_FAST) ro-diff-core.txt + $(MAKE_FAST) ro-diff.txt + +grepro: + cat ro-diff.txt | grep /RO_ > ro-diff.txt.ro.txt + cat ro-diff-core.txt | grep /RO_ > ro-diff-core.txt.ro.txt + +# ======================================== +# MIREOT +# ======================================== + +bfo2-classes.owl: + $(OWLTOOLS) $(URIBASE)/bfo.owl --make-subset-by-properties // --set-ontology-id $(URIBASE)/ro/bfo2-classes.owl -o file://`pwd`/bfo2-classes.owl + +# ======================================== +# SUBSETS +# ======================================== + +# generated by oort: +subsets/ro-eco.owl: build/subsets/ro-eco.owl + $(OWLTOOLS) --use-catalog $< --remove-dangling -o $@ + +subsets/ro-biotic-interaction.owl: ro.owl + $(ROBOT) filter -i $< --term RO:0002437 --select "annotations self descendants" -o $@.tmp.owl && mv $@.tmp.owl $@ + +# the following subsets are generated purely by hierarchy: +subsets/ro-interaction.owl: ro.owl + $(OWLTOOLS) --use-catalog $< --extract-properties -s --list 'interacts with' // --set-ontology-id $(URIBASE)/ro/$@ -o $@ +subsets/ro-sequence.owl: ro.owl + $(OWLTOOLS) --use-catalog $< --extract-properties -s --list 'sequentially related to' // --set-ontology-id $(URIBASE)/ro/$@ -o $@ +subsets/ro-time-interval.owl: ro.owl + $(OWLTOOLS) --use-catalog $< --extract-properties -s --list 'temporally related to' // --set-ontology-id $(URIBASE)/ro/$@ -o $@ +subsets/ro-mereotopology.owl: ro.owl + $(OWLTOOLS) --use-catalog $< --extract-properties -s --list 'mereotopologically related to' // --set-ontology-id $(URIBASE)/ro/$@ -o $@ +subsets/ro-causal.owl: ro.owl + $(OWLTOOLS) --use-catalog $< --extract-properties -s --list 'causally related to' // --set-ontology-id $(URIBASE)/ro/$@ -o $@ +subsets/ro-developmental.owl: ro.owl + $(OWLTOOLS) --use-catalog $< --extract-properties -s --list 'developmentally related to' // --set-ontology-id $(URIBASE)/ro/$@ -o $@ +#subsets/ro-eco.owl: ro.owl +# $(OWLTOOLS) --use-catalog $< --extract-properties -s --list 'ecologically related to' // --set-ontology-id $(URIBASE)/ro/$@ -o $@ +subsets/ro-hom.owl: ro.owl + $(OWLTOOLS) --use-catalog $< --extract-properties -s --list 'in similarity relationship with' // --set-ontology-id $(URIBASE)/ro/$@ -o $@ + +subsets/%.csv: subsets/%.owl + $(ROBOT) query -i $< -s $(SPARQLDIR)/objectProperties.sparql $@.tmp -f csv && mv $@.tmp $@ + +subsets/ro-chado.obo: ro.obo + $(OWLTOOLS) --use-catalog $< --merge-imports-closure --remove-tbox --remove-annotation-assertions -r -l -s -d --remove-dangling --set-ontology-id $(URIBASE)/ro/$@ -o -f obo $@.tmp && ../tools/translate-to-chado-obo.pl $@.tmp > $@ && rm $@.tmp + +# ======================================== +# REPORTING (EXPERIMENTAL) +# ======================================== +# requires sparqlprog + +usage.tsv: ro-base.owl + pq-ontobee -f tsv -e -i $< "owl:objectProperty(P), label(P,PN), (ontobee ?? aggregate_group(count(Restr),[P,G],rdf(Restr,owl:onProperty,P,G),Num))" "x(P,PN,G,Num)" > $@.tmp && mv $@.tmp $@ +usage-full.tsv: + pq-ontobee -f tsv -e -i ro.owl "owl:objectProperty(P), (ontobee ?? rdf(Restr,owl:onProperty,P,G),label(P,PN))" "x(Restr,P,PN,G)" > $@.tmp && mv $@.tmp $@ + +# ======================================== +# EXPERIMENTAL +# ======================================== + +# Oort requires more testing before it can be used for a relations ontology. +# for now, just go with a simple release process (see above) +build-using-oort: ro-edit.owl + ontology-release-runner --catalog-xml catalog-v001.xml --outdir build --simple --allow-overwrite --reasoner hermit ro-edit.owl + touch $@ + +hom.obo: + wget $(URIBASE)/hom.obo -O $@.tmp && mv $@.tmp $@ +hom-fixed.obo: hom.obo + obo-grep.pl --neg -r is_obsolete: $< > $@.tmp && mv $@.tmp $@ + +rohom.obo: hom-fixed.obo + ../tools/hom2rhom.pl $< > $@.tmp && mv $@.tmp $@ +rohom.owl: rohom.obo + $(OWLTOOLS) $< -o $@.tmp && grep -v 'oboInOwl:id' $@.tmp > $@.tmp2 && $(HOME)/repos/uberon/util/expand-dbxref-literals.pl $@.tmp2 > $@ + +## ODPs + +odp/%.owl: + wget http://www.ontologydesignpatterns.org/cp/owl/$*.owl -O $@ + + +# ---------------------------------------- +# Reports +# ---------------------------------------- +REPORTS=basicReport +all_reports: $(patsubst %, reports/envo-%.csv, $(REPORTS)) reports/ro.owl-obo-report.tsv + +reports/ro-%.csv: $(SPARQLDIR)/%.sparql ro.owl + $(ROBOT) query -i ro.owl -s $< $@.tmp -f csv && mv $@.tmp $@ + +# SPARQL constructs +$(REPORTDIR)/ro-%.ttl: $(SPARQLDIR)/%.sparql ro.owl + $(ROBOT) query -i ro.owl -c $< $@.tmp.ttl -f ttl annotate -O $(URIBASE)/ro/$@ -o $@ + +views/%.owl: $(SPARQLDIR)/%.sparql ro.owl + $(ROBOT) merge -i ro.owl query -c $< $@.tmp.ttl -f ttl annotate -O $(URIBASE)/ro/$@ -o $@ + +gen-%.owl: $(SPARQLDIR)/construct-%.sparql ro.owl + $(ROBOT) query -i ro.owl -c $< $@.tmp.ttl -f ttl annotate -O $(URIBASE)/ro/$@ -o $@ + +# See https://github.com/oborel/obo-relations/pull/270 +GENAXIOMS = gen-universal-from-homeomorphy.owl +generated-axioms.owl: $(GENAXIOMS) + $(ROBOT) merge $(patsubst %, -i %, $(GENAXIOMS)) -o $@.tmp.ttl annotate -O $(URIBASE)/ro/$@ -o $@ + +# generate includes from sparql CONSTRUCT queries; +# these can then be merged in to the main ontology +#reports/include-%.owl: $(SPARQLDIR)/construct-%.sparql ecto-core.owl + +# ---------------------------------------- +# MARKDOWN EXPORT +# ---------------------------------------- +markdown: ro.owl + $(OWLTOOLS) $< --merge-imports-closure --ontology-to-markdown -l 0 md + diff --git a/src/ontology/rohom.owl b/src/ontology/rohom.owl deleted file mode 100644 index f48e567e..00000000 --- a/src/ontology/rohom.owl +++ /dev/null @@ -1,1723 +0,0 @@ - - - - 1.2 - - - - - - - - - - - - - definition - - - - - - - - - - - - - - - - - - - - has_broad_synonym - - - - - - - - database_cross_reference - - - - - - - - has_exact_synonym - - - - - - - - has_obo_format_version - - - - - - - - has_related_synonym - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - in similarity relationship with - ECO:0000041 - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - SO:similar_to - correspondence - resemblance - sameness - similar to - - - - - - - correspondence - - - - - BGEE:curator - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - - - - - - - - - - in homology relationship with - Similarity that results from common evolutionary origin. - This broad definition encompasses all the working definitions proposed so far in the literature. - homologous to - - - - - - - - - - - - Similarity that results from common evolutionary origin. - - - - - - - - - - - in homoplasy relationship with - Similarity that results from independent evolution. - analogy - homoplasous to - - - - - - - - - Similarity that results from independent evolution. - - - - - - - - - - - in homocracy relationship with - ECO:0000075 - Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - homocracous to - - - - - - - - - - - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - - - - - - - - - - in convergence relationship with - Convergence usually implies a notion of adaptation. - Homoplasy that involves different underlying mechanisms or structures. - analogy - - - - - - - - - Homoplasy that involves different underlying mechanisms or structures. - - - - - - - - - - - in parallelism relationship with - Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. - Homoplasy that involves homologous underlying mechanisms or structures. - parallel evolution - - - - - - - - - Homoplasy that involves homologous underlying mechanisms or structures. - - - - - - - - - - - in structural homology relationship with - ECO:0000071 - Homology that is defined by similarity with regard to selected structural parameters. - MI:2163 - idealistic homology - structural homologous to - - - - - - - - - - Homology that is defined by similarity with regard to selected structural parameters. - ISBN:0123195837 - - - - - - - - - - - in historical homology relationship with - ECO:0000080 - Homology that is defined by common descent. - RO_proposed_relation:homologous_to - SO:0000330 - SO:0000853 - SO:0000857 - SO:homologous_to - TAO:homologous_to - cladistic homology - historical homologous to - homology - phylogenetic homology - taxic homology - true homology - - - - - - - - - Homology that is defined by common descent. - ISBN:0123195837 - - - - - - - - - - - in biological homology relationship with - Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. - ECO:0000067 - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - biological homologous to - transformational homology - - - - - - - - - - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - - - - - - - - - - in reversal relationship with - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - atavism - reversion - rudiment - - - - - - - - - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - - - - - - - - - - in syntenic homology relationship with - MeSH:Synteny - SO:0000860 - SO:0005858 - Structural homology that is detected by similarity in content and organization between chromosomes. - syntenic homologous to - synteny - - - - - - - - MeSH:Synteny - Structural homology that is detected by similarity in content and organization between chromosomes. - - - - - - - - - - - in paralogy relationship with - Historical homology that involves genes that diverged after a duplication event. - SO:0000854 - SO:0000859 - SO:paralogous_to - paralogous to - - - - - - - - - - - Historical homology that involves genes that diverged after a duplication event. - - - - - - - - - - - - in syntenic paralogy relationship with - Paralogy that involves sets of syntenic blocks. - duplicon - paralogon - syntenic paralogous to - - - - - - - - DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y - - - Paralogy that involves sets of syntenic blocks. - - - - - - - - - - - in syntenic orthology relationship with - Syntenic homology that involves chromosomes of different species. - syntenic orthologous to - - - - - - - - - Syntenic homology that involves chromosomes of different species. - - - - - - - - - - - in partial homology relationship with - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - fractional homology - mixed homology - modular homology - partial correspondence - partial homologous to - percent homology - segmental homology - - - - - - - - ISBN:0123195837 - ISBN:978-0471984931 - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - - - - - - - - - - in protein structural homology relationship with - MeSH:Structural_Homology,_Protein - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - protein structural homologous to - - - - - - - - - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - - - - - - - - - - in non functional homology relationship with - SO:non_functional_homolog_of - Structural homology that involves a pseudogenic feature and its functional ancestor. - non functional homologous to - pseudogene - - - - - - - - - SO:non_functional_homolog_of - Structural homology that involves a pseudogenic feature and its functional ancestor. - - - - - - - - - - - in orthology relationship with - ECO:00000060 - Historical homology that involves genes that diverged after a speciation event. - SO:0000855 - SO:0000858 - SO:orthologous_to - The term is sometimes also used for anatomical structures. - orthologous to - - - - - - - - - - - Historical homology that involves genes that diverged after a speciation event. - - - - - - - - - - - - in xenology relationship with - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). - xenologous to - - - - - - - - - - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - - - - - - - - - - in 1 to 1 homology relationship with - 1 to 1 homologous to - 1:1 homology - Historical homology that involves two members sharing no other homologs in the lineages considered. - one-to-one homology - - - - - - - BGEE:curator - - Historical homology that involves two members sharing no other homologs in the lineages considered. - - - - - - - - - - - in 1 to 1 orthology relationship with - 1 to 1 orthologous to - 1:1 orthology - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - one-to-one orthology - - - - - - - - - - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - - - - - - - - - - - in ohnology relationship with - Paralogy that results from a whole genome duplication event. - homoeology - ohnologous to - - - - - - - - - Paralogy that results from a whole genome duplication event. - - - - - - - - - - - in in-paralogy relationship with - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - in-paralogous to - inparalogy - symparalogy - - - - - - - - - - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - - - - - - - - - - in out-paralogy relationship with - Paralogy that results from a duplication preceding a given speciation event. - alloparalogy - out-paralogous to - outparalogy - - - - - - - - - Paralogy that results from a duplication preceding a given speciation event. - - - - - - - - - - - in pro-orthology relationship with - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - pro-orthologous to - - - - - - - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - - - - - - - - - - - - - in semi-orthology relationship with - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - The converse of pro-orthologous. - semi-orthologous to - - - - - - - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - - - - - - - - - - - - - in serial homology relationship with - Iterative homology that involves structures arranged along the main body axis. - homonomy - serial homologous to - - - - - - - - - Iterative homology that involves structures arranged along the main body axis. - - - - - - - - - - - in heterochronous homology relationship with - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - heterochronous homologous to - heterochrony - - - - - - - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - ISBN:978-0674639416 - - - - - - - - - - - in paedomorphorsis relationship with - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - juvenification - pedomorphosis - - - - - - - - - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - ISBN:978-0674639416 - - - - - - - - - - - - in peramorphosis relationship with - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - - - - - - - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - - - - - - - - - - - in progenesis relationship with - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - - - - - - - ISBN:978-0674639416 - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - - - - - - - - - - - in neoteny relationship with - Paedomorphosis that is produced by a retardation of somatic development. - juvenilization - neotenous to - - - - - - - - ISBN:978-0674639416 - Paedomorphosis that is produced by a retardation of somatic development. - - - - - - - - - - - - in mimicry relationship with - Convergence that results from co-evolution usually involving an evolutionary arms race. - mimicrous to - - - - - - - Convergence that results from co-evolution usually involving an evolutionary arms race. - - - - - - - - - - - - - in 1 to many orthology relationship with - 1 to many orthologous to - 1:many orthology - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - co-orthology - many to 1 orthology - one-to-many orthology - - - - - - - - - - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - - - - - - - - - - - in many to many homology relationship with - Historical homology that involves two members of a larger set of homologs. - many to many homologous to - many-to-many homology - many:many homology - - - - - - - - - Historical homology that involves two members of a larger set of homologs. - - - - - - - - - - - in 1 to many homology relationship with - 1 to many homologous to - 1:many homology - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - one-to-many homology - - - - - - - BGEE:curator - - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - - - - - - - - - - in apomorphy relationship with - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - apomorphous to - synapomorphy - - - - - - - - - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - ISBN:978-0252068140 - - - - - - - - - - - in plesiomorphy relationship with - Historical homology that is based on distant shared ancestry. - This term is usually contrasted to apomorphy. - plesiomorphous to - symplesiomorphy - - - - - - - - Historical homology that is based on distant shared ancestry. - ISBN:978-0252068140 - - - - - - - - - - - in deep homology relationship with - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - Used for structures in distantly related taxa. - deep genetic homology - deep homologous to - generative homology - homoiology - - - - - - - - - - - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - - - - - - - - - - in hemiplasy relationship with - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - hemiplasous to - - - - - - - - - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - - - - - - - - - - in gametology relationship with - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - gametologous to - - - - - - - - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - - - - - - - - - - - in chromosomal homology relationship with - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - MeSH:Chromosome_Pairing - chromosomal homologous to - - - - - - - - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - ISBN:0195307615 - - - - - - - - - - - in many to many orthology relationship with - Orthology that involves two genes that experienced duplications more recent than the species split that created them. - co-orthology - many to many orthologous to - many-to-many orthology - many:many orthology - trans-homology - trans-orthology - - - - - - - - - - Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - - - - - - - - - - - in within-species paralogy relationship with - Paralogy that involves genes from the same species. - within-species paralogous to - - - - - - - - - Paralogy that involves genes from the same species. - - - - - - - - - - - - in between-species paralogy relationship with - Paralogy that involves genes from different species. - The genes have diverged before a speciation event. - between-species paralogous to - - - - - - - - Paralogy that involves genes from different species. - - - - - - - - - - - - in postdisplacement relationship with - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - post-displacement - - - - - - - - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - - - - - - - - - - - in hypermorphosis relationship with - Peramorphosis that is produced by a delay in the offset of development. - - - - - - - - ISBN:978-0674639416 - Peramorphosis that is produced by a delay in the offset of development. - - - - - - - - - - - - in synology relationship with - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - synologous to - - - - - - - - - - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - - - - - - - - - - in isoorthology relationship with - ECO:0000080 - Orthology that involves functional equivalent genes with retention of the ancestral function. - isoorthologous to - - - - - - - - - - Orthology that involves functional equivalent genes with retention of the ancestral function. - - - - - - - - - - - in tandem paralogy relationship with - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - iterative paralogy - serial paralogy - tandem paralogous to - - - - - - - - - ISBN:978-0878932665 - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - - - - - - - - - - in latent homology relationship with - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - Used for structures in closely related taxa. - apomorphic tendency - cryptic homology - homoiology - homoplastic tendency - latent homologous to - re-awakening - underlying synapomorphy - - - - - - - - - - - - ISBN:0199141118 - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - - - - - - - - - - in syngeny relationship with - Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - generative homology - syngenous to - - - - - - - DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R - - - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - - - - - - - - - - in apparent orthology relationship with - 1:1 paralogy - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. - apparent 1:1 orthology - apparent orthologous to - pseudoorthology - - - - - - - - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - - - - - - - - - - - - - in pseudoparalogy relationship with - These genes may come out as paralogs in a single-genome analysis. - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - pseudoparalogous to - - - - - - - - - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - - - - - - - - - - in equivalogy relationship with - Historical homology that involves functional equivalent genes with retention of the ancestral function. - This may include examples of orthology, paralogy and xenology. - equivalogous to - - - - - - - - - - Historical homology that involves functional equivalent genes with retention of the ancestral function. - - - - - - - - - - - in interology relationship with - Historical homology that involves orthologous pairs of interacting molecules in different organisms. - interologous to - - - - - - - - - - Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - - - - - - - - - - in functional equivalence relationship with - Similarity that is characterized by interchangeability in function. - functional similarity - - - - - - - - - - Similarity that is characterized by interchangeability in function. - - - - - - - - - - - in iterative homology relationship with - Biological homology that involves parts of the same organism. - iterative homologous to - - - - - - - Biological homology that involves parts of the same organism. - - - - - - - - - - - - - in paraxenology relationship with - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - duplicate xenology - multiple xenology - paraxenologous to - - - - - - - - - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - - - - - - - - - - in plerology relationship with - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - This phenomenon is usually due to gene conversion process. - plerologous to - - - - - - - - - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - - - - - - - - - - in homotopy relationship with - Structural homology that involves structures with the same or similar relative positions. - Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. - homotopous to - - - - - - - - - - - ISBN:0123195837 - Structural homology that involves structures with the same or similar relative positions. - - - - - - - - - - - in homeosis relationship with - Biological homology that involves an ectopic structure and the normally positioned structure. - heterotopy - - - - - - - Biological homology that involves an ectopic structure and the normally positioned structure. - - - - - - - - - - - - - - in homoeology relationship with - On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. - Synology that results from allopolyploidy. - homoeologous to - - - - - - - - - - Synology that results from allopolyploidy. - - - - - - - - - - - in paramorphism relationship with - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - axis paramorphism - - - - - - - - - - - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - - - - - - - - - - in regulogy relationship with - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - regulogous to - - - - - - - - - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - - - - - - - - diff --git a/src/ontology/run.bat b/src/ontology/run.bat new file mode 100644 index 00000000..ce0179f1 --- /dev/null +++ b/src/ontology/run.bat @@ -0,0 +1 @@ +docker run -v %cd%\..\..\:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx8G' -e JAVA_OPTS='-Xmx8G' --rm -ti obolibrary/odkfull %* \ No newline at end of file diff --git a/src/ontology/run.sh b/src/ontology/run.sh index c0eaad8b..2718ff67 100755 --- a/src/ontology/run.sh +++ b/src/ontology/run.sh @@ -8,8 +8,70 @@ # The assumption is that you are working in the src/ontology folder; # we therefore map the whole repo (../..) to a docker volume. # +# To use singularity instead of docker, please issue +# export USE_SINGULARITY= +# before running this script. +# # See README-editors.md for more details. -IMAGE=${IMAGE:-odkfull} +if [ -f run.sh.conf ]; then + . ./run.sh.conf +fi + +# Look for a GitHub token +if [ -n "$GH_TOKEN" ]; then + : +elif [ -f ../../.github/token.txt ]; then + GH_TOKEN=$(cat ../../.github/token.txt) +elif [ -f $XDG_CONFIG_HOME/ontology-development-kit/github/token ]; then + GH_TOKEN=$(cat $XDG_CONFIG_HOME/ontology-development-kit/github/token) +elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/token" ]; then + GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token") +fi + +ODK_IMAGE=${ODK_IMAGE:-odkfull} +TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }') +if [ -n "$TAG_IN_IMAGE" ]; then + # Override ODK_TAG env var if IMAGE already includes a tag + ODK_TAG=$TAG_IN_IMAGE + ODK_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $1 }') +fi +ODK_TAG=${ODK_TAG:-latest} +ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G} +ODK_DEBUG=${ODK_DEBUG:-no} + +TIMECMD= +if [ x$ODK_DEBUG = xyes ]; then + # If you wish to change the format string, take care of using + # non-breaking spaces (U+00A0) instead of normal spaces, to + # prevent the shell from tokenizing the format string. + echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps." + TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb" +fi + +VOLUME_BIND=$PWD/../../:/work +WORK_DIR=/work/src/ontology + +if [ -n "$ODK_BINDS" ]; then + VOLUME_BIND="$VOLUME_BIND,$ODK_BINDS" +fi + +if [ -n "$USE_SINGULARITY" ]; then + + singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \ + --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \ + --bind $VOLUME_BIND \ + -W $WORK_DIR \ + docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" +else + BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')" + docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \ + -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \ + --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" +fi -docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx12G' -e JAVA_OPTS='-Xmx12G' --rm -ti obolibrary/$IMAGE "$@" \ No newline at end of file +case "$@" in +*update_repo*|*release*) + echo "Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/." + ;; +esac \ No newline at end of file diff --git a/src/ontology/sparql/terms.sparql b/src/ontology/sparql/terms.sparql deleted file mode 100644 index e65a105a..00000000 --- a/src/ontology/sparql/terms.sparql +++ /dev/null @@ -1,7 +0,0 @@ -SELECT DISTINCT ?term -WHERE { - { ?s1 ?p1 ?term . } - UNION - { ?term ?p2 ?o2 . } - FILTER(isIRI(?term)) -} \ No newline at end of file diff --git a/src/ontology/subsets/ro-biotic-interaction.json b/src/ontology/subsets/ro-biotic-interaction.json new file mode 100644 index 00000000..8309ba7d --- /dev/null +++ b/src/ontology/subsets/ro-biotic-interaction.json @@ -0,0 +1,1137 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002437", + "lbl" : "biotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "interacts with on organism level" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/interactsWith" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002438", + "lbl" : "trophically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the partners are related via a feeding relationship." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "lbl" : "preys on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Baleen whale preys on krill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7134-3324" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of predation interaction with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preys upon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/preysUpon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.inaturalist.org/observations/2942824" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002440", + "lbl" : "symbiotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction in which the two organisms live together in more or less intimate association." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002441", + "lbl" : "commensually interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002442", + "lbl" : "mutualistically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "lbl" : "interacts with via parasite-host interaction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002444", + "lbl" : "parasite of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "direct parasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Pediculus humanus capitis parasite of human" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitizes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/parasitizes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002445", + "lbl" : "parasitized by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "directly parasitized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "semibiotically interacts with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Porifiera attaches to substrate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002453", + "lbl" : "host of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "lbl" : "has host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasHost" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002455", + "lbl" : "pollinates", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Bees pollinate Flowers" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/pollinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "lbl" : "pollinated by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has polinator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasPollinator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "lbl" : "acquires nutrients from", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002458", + "lbl" : "preyed upon by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of preys on" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has predator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of predation interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/HasPredator" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "lbl" : "is vector for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002460", + "lbl" : "has vector", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002553", + "lbl" : "hyperparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "hyperparasitoid of" + }, { + "pred" : "hasRelatedSynonym", + "val" : "epiparasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://eol.org/schema/terms/hyperparasitoidOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Hyperparasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "lbl" : "hyperparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of hyperparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "has epiparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has hyperparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hyperparasitoidized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002555", + "lbl" : "allelopath of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Allelopathy" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/allelopathyYes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002556", + "lbl" : "pathogen of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002557", + "lbl" : "has pathogen", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002574", + "lbl" : "participates in a biotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002618", + "lbl" : "visits", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/74" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002619", + "lbl" : "visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002622", + "lbl" : "visits flowers of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002623", + "lbl" : "has flowers visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002624", + "lbl" : "lays eggs in", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002625", + "lbl" : "has eggs laid in by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002626", + "lbl" : "kills", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://github.com/jhpoelen/eol-globi-data/issues/143" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002627", + "lbl" : "is killed by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002632", + "lbl" : "ectoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002633", + "lbl" : "has ectoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ectoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002634", + "lbl" : "endoparasite of", + "type" : "PROPERTY", + "meta" : { + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "lives inside of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002635", + "lbl" : "has endoparasite", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002636", + "lbl" : "mesoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002637", + "lbl" : "has mesoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of mesoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002638", + "lbl" : "intercellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002639", + "lbl" : "has intercellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intercellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002640", + "lbl" : "intracellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002641", + "lbl" : "has intracellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intracellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008501", + "lbl" : "epiphyte of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Epiphyte" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008502", + "lbl" : "has epiphyte", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of epiphyte of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008503", + "lbl" : "kleptoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008504", + "lbl" : "kleptoparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of kleptoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008507", + "lbl" : "lays eggs on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008508", + "lbl" : "has eggs laid on by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of lays eggs on" + } + } + } ], + "edges" : [ { + "sub" : "http://purl.obolibrary.org/obo/RO_0002208", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002209", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002445" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002227", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002228", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002235", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002236", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002237", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002438", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002439", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002440", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002441", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002442", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002443", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002444", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002443" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002444", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002445", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002443" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002445", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002446", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002453", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002454", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002455", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002442" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002456", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002442" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002457", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002458", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002459", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002460", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002469", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002470", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002471", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002438" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002553", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002554", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002555", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002556", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002454" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002557", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002453" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002574", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002437" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002618", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002619", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002622", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002618" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002623", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002624", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002624", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002618" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002625", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002445" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002625", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002626", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002627", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002574" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002632", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002633", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002445" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002634", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002635", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002445" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002636", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002637", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002445" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002638", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002634" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002639", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002635" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002640", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002634" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002641", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002635" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008501", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008502", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002440" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008503", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002444" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008504", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002445" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008507", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002618" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008508", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002208", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002209" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002439", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002458" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002444", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002445" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002455", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002456" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002457", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002469" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002459", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002460" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002553", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002554" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002556", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002557" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002618", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002619" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002622", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002623" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002624", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002625" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002626", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002627" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002632", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002633" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002634", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002635" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002636", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002637" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002638", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002639" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002640", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008501", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0008502" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008503", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0008504" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008507", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0008508" + } ], + "propertyChainAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002553", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002444", "http://purl.obolibrary.org/obo/RO_0002444" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002554", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002445", "http://purl.obolibrary.org/obo/RO_0002445" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/subsets/ro-biotic-interaction.obo b/src/ontology/subsets/ro-biotic-interaction.obo new file mode 100644 index 00000000..1f33ac3f --- /dev/null +++ b/src/ontology/subsets/ro-biotic-interaction.obo @@ -0,0 +1,486 @@ +format-version: 1.2 +ontology: ro + +[Typedef] +id: RO:0002208 +name: parasitoid of +def: "A parasite that kills or sterilizes its host" [] +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002209 ! has parasitoid + +[Typedef] +id: RO:0002209 +name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002227 +name: obligate parasite of +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002228 +name: facultative parasite of +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002235 +name: stem parasite of +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002236 +name: root parasite of +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002237 +name: hemiparasite of +def: "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002437 +name: biotically interacts with +def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "interacts with on organism level" xsd:string +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string +is_symmetric: true + +[Typedef] +id: RO:0002438 +name: trophically interacts with +def: "An interaction relationship in which the partners are related via a feeding relationship." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002439 +name: preys on +def: "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" [] +subset: ro-eco +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string +property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000118 "is subject of predation interaction with" xsd:string +property_value: IAO:0000118 "preys upon" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string +is_a: RO:0002438 ! trophically interacts with +inverse_of: RO:0002458 ! preyed upon by + +[Typedef] +id: RO:0002440 +name: symbiotically interacts with +def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string +is_symmetric: true +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002441 +name: commensually interacts with +def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002442 +name: mutualistically interacts with +def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002443 +name: interacts with via parasite-host interaction +def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002444 +name: parasite of +subset: ro-eco +synonym: "direct parasite of" EXACT [] +property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "parasitizes" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string +is_a: RO:0002443 ! interacts with via parasite-host interaction +is_a: RO:0002454 ! has host +inverse_of: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002445 +name: parasitized by +subset: ro-eco +synonym: "directly parasitized by" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has parasite" xsd:string +property_value: IAO:0000118 "parasitised by" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string +is_a: RO:0002443 ! interacts with via parasite-host interaction +is_a: RO:0002453 ! host of + +[Typedef] +id: RO:0002446 +name: participates in a abiotic-biotic interaction with +def: "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." [] +subset: ro-eco +synonym: "semibiotically interacts with" RELATED [] +property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +is_a: RO:0002437 ! biotically interacts with + +[Typedef] +id: RO:0002453 +name: host of +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002454 +name: has host +def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002455 +name: pollinates +subset: ro-eco +property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string +property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string +is_a: RO:0002442 ! mutualistically interacts with +inverse_of: RO:0002456 ! pollinated by + +[Typedef] +id: RO:0002456 +name: pollinated by +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has polinator" xsd:string +property_value: IAO:0000118 "is target of pollination interaction with" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string +is_a: RO:0002442 ! mutualistically interacts with + +[Typedef] +id: RO:0002457 +name: acquires nutrients from +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string +is_a: RO:0002438 ! trophically interacts with +inverse_of: RO:0002469 ! provides nutrients for + +[Typedef] +id: RO:0002458 +name: preyed upon by +def: "inverse of preys on" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has predator" xsd:string +property_value: IAO:0000118 "is target of predation interaction with" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002459 +name: is vector for +subset: ro-eco +property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string +is_a: RO:0002574 ! participates in a biotic-biotic interaction with +inverse_of: RO:0002460 ! has vector + +[Typedef] +id: RO:0002460 +name: has vector +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002469 +name: provides nutrients for +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002470 +name: eats +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "is subject of eating interaction with" xsd:string +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002471 +name: is eaten by +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "eaten by" xsd:string +property_value: IAO:0000118 "is target of eating interaction with" xsd:string +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002553 +name: hyperparasite of +def: "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" [] +subset: ro-eco +synonym: "epiparasite of" RELATED [] +synonym: "hyperparasitoid of" NARROW [] +property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string +holds_over_chain: RO:0002444 RO:0002444 +is_a: RO:0002454 ! has host +inverse_of: RO:0002554 ! hyperparasitized by + +[Typedef] +id: RO:0002554 +name: hyperparasitized by +def: "inverse of hyperparasite of" [] +subset: ro-eco +subset: RO:0002259 +synonym: "has epiparasite" RELATED [] +synonym: "has hyperparasite" RELATED [] +synonym: "hyperparasitoidized by" RELATED [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002445 RO:0002445 +is_a: RO:0002453 ! host of + +[Typedef] +id: RO:0002555 +name: allelopath of +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string +property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002556 +name: pathogen of +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002454 ! has host +inverse_of: RO:0002557 ! has pathogen + +[Typedef] +id: RO:0002557 +name: has pathogen +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002453 ! host of + +[Typedef] +id: RO:0002574 +name: participates in a biotic-biotic interaction with +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +is_a: RO:0002437 ! biotically interacts with + +[Typedef] +id: RO:0002618 +name: visits +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI +is_a: RO:0002574 ! participates in a biotic-biotic interaction with +inverse_of: RO:0002619 ! visited by + +[Typedef] +id: RO:0002619 +name: visited by +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002622 +name: visits flowers of +is_a: RO:0002618 ! visits +inverse_of: RO:0002623 ! has flowers visited by + +[Typedef] +id: RO:0002623 +name: has flowers visited by +is_a: RO:0002619 ! visited by + +[Typedef] +id: RO:0002624 +name: lays eggs in +is_a: RO:0002444 ! parasite of +is_a: RO:0002618 ! visits +inverse_of: RO:0002625 ! has eggs laid in by + +[Typedef] +id: RO:0002625 +name: has eggs laid in by +is_a: RO:0002445 ! parasitized by +is_a: RO:0002619 ! visited by + +[Typedef] +id: RO:0002626 +name: kills +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string +is_a: RO:0002574 ! participates in a biotic-biotic interaction with +inverse_of: RO:0002627 ! is killed by + +[Typedef] +id: RO:0002627 +name: is killed by +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002632 +name: ectoparasite of +def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] +property_value: IAO:0000119 Types +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002633 ! has ectoparasite + +[Typedef] +id: RO:0002633 +name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002634 +name: endoparasite of +synonym: "lives inside of" RELATED [] +property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string +property_value: IAO:0000119 Types +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002635 ! has endoparasite + +[Typedef] +id: RO:0002635 +name: has endoparasite +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002636 +name: mesoparasite of +def: "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" [] +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002637 ! has mesoparasite + +[Typedef] +id: RO:0002637 +name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002638 +name: intercellular endoparasite of +def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] +property_value: IAO:0000119 Types +is_a: RO:0002634 ! endoparasite of +inverse_of: RO:0002639 ! has intercellular endoparasite + +[Typedef] +id: RO:0002639 +name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 +is_a: RO:0002635 ! has endoparasite + +[Typedef] +id: RO:0002640 +name: intracellular endoparasite of +def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] +property_value: IAO:0000119 Types +is_a: RO:0002634 ! endoparasite of +inverse_of: RO:0002641 ! has intracellular endoparasite + +[Typedef] +id: RO:0002641 +name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 +is_a: RO:0002635 ! has endoparasite + +[Typedef] +id: RO:0008501 +name: epiphyte of +def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string +is_a: RO:0002440 ! symbiotically interacts with +inverse_of: RO:0008502 ! has epiphyte + +[Typedef] +id: RO:0008502 +name: has epiphyte +def: "inverse of epiphyte of" [] +subset: RO:0002259 +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0008503 +name: kleptoparasite of +def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string +is_a: RO:0002444 ! parasite of +inverse_of: RO:0008504 ! kleptoparasitized by + +[Typedef] +id: RO:0008504 +name: kleptoparasitized by +def: "inverse of kleptoparasite of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0008507 +name: lays eggs on +def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] +is_a: RO:0002618 ! visits +inverse_of: RO:0008508 ! has eggs laid on by + +[Typedef] +id: RO:0008508 +name: has eggs laid on by +def: "inverse of lays eggs on" [] +is_a: RO:0002619 ! visited by + diff --git a/src/ontology/subsets/ro-biotic-interaction.owl b/src/ontology/subsets/ro-biotic-interaction.owl index 76d94dfd..9017b92f 100644 --- a/src/ontology/subsets/ro-biotic-interaction.owl +++ b/src/ontology/subsets/ro-biotic-interaction.owl @@ -65,21 +65,15 @@ - + - + - + - - - - - - - + @@ -183,7 +177,7 @@ An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level biotically interacts with @@ -198,7 +192,7 @@ An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + trophically interacts with @@ -214,9 +208,9 @@ A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon @@ -233,10 +227,9 @@ A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - symbiotically interacts with @@ -248,9 +241,8 @@ An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 - commensually interacts with @@ -262,9 +254,8 @@ An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 - mutualistically interacts with @@ -276,10 +267,9 @@ An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by - interacts with via parasite-host interaction @@ -293,9 +283,8 @@ Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes - direct parasite of parasite of @@ -309,7 +298,7 @@ - Chris Mungall + has parasite parasitised by directly parasitized by @@ -326,7 +315,7 @@ Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + semibiotically interacts with participates in a abiotic-biotic interaction with @@ -339,8 +328,7 @@ - - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) host of @@ -352,8 +340,8 @@ - - Chris Mungall + X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y + has host http://eol.org/schema/terms/hasHost @@ -368,7 +356,7 @@ Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with pollinates @@ -381,7 +369,7 @@ - Chris Mungall + has polinator is target of pollination interaction with @@ -396,7 +384,7 @@ - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. acquires nutrients from @@ -409,7 +397,7 @@ inverse of preys on - Chris Mungall + has predator is target of predation interaction with @@ -427,7 +415,7 @@ Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism is vector for @@ -439,7 +427,7 @@ - Chris Mungall + has vector @@ -450,7 +438,7 @@ - Chris Mungall + provides nutrients for @@ -461,7 +449,7 @@ - Chris Mungall + is subject of eating interaction with eats @@ -473,7 +461,7 @@ - Chris Mungall + eaten by is target of eating interaction with @@ -493,11 +481,11 @@ x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite + hyperparasitoid of epiparasite of - hyperparasitoid of hyperparasite of @@ -513,7 +501,7 @@ inverse of hyperparasite of - Chris Mungall + has epiparasite has hyperparasite hyperparasitoidized by @@ -528,7 +516,7 @@ - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy allelopath of @@ -543,7 +531,7 @@ - Chris Mungall + pathogen of @@ -554,7 +542,7 @@ - Chris Mungall + has pathogen @@ -565,7 +553,7 @@ - Chris Mungall + participates in a biotic-biotic interaction with @@ -576,7 +564,6 @@ - visits @@ -588,7 +575,6 @@ - visited by @@ -829,12 +815,12 @@ - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. + inverse of lays eggs on has eggs laid on by - + diff --git a/src/ontology/subsets/ro-biotic-interaction.tsv b/src/ontology/subsets/ro-biotic-interaction.tsv new file mode 100644 index 00000000..e69de29b diff --git a/src/ontology/subsets/ro-causal.json b/src/ontology/subsets/ro-causal.json new file mode 100644 index 00000000..7e8d7fb2 --- /dev/null +++ b/src/ontology/subsets/ro-causal.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-causal.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_2D_boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_2D_boundary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "lbl" : "electrically_synapsed_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions." + }, + "xrefs" : [ { + "val" : "RO:0002003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "electrically_synapsed_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002007" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "lbl" : "coincident with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." + }, + "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002008" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note from NCEAS meeting: consider changing primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "coincident_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "lbl" : "regulates in other organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "xrefs" : [ { + "val" : "RO:0002010" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_in_other_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "lbl" : "occurrent part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A part of relation that applies only between occurrents." + }, + "xrefs" : [ { + "val" : "RO:0002012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurrent_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." + }, + "xrefs" : [ { + "val" : "RO:0002013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "xrefs" : [ { + "val" : "RO:0002014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_negative_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], + "xrefs" : [ { + "val" : "RO:0002015" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_positive_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "lbl" : "has necessary component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], + "xrefs" : [ { + "val" : "RO:0002016" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_necessary_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], + "xrefs" : [ { + "val" : "RO:0002017" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:44:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "xrefs" : [ { + "val" : "RO:0002018" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "lbl" : "has ligand", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." + }, + "xrefs" : [ { + "val" : "RO:0002019" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-19T17:30:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ligand" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "lbl" : "transports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." + }, + "xrefs" : [ { + "val" : "RO:0002020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:11:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." + }, + "xrefs" : [ { + "val" : "RO:0002021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "xrefs" : [ { + "val" : "RO:0002022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:38Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. 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No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." + }, + "xrefs" : [ { + "val" : "RO:0002104" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : 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"synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002106" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that 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it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002113" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "synapses in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_presynaptic_terminal_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002114", + "lbl" : "synapsed_via_type_III_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." + }, + "comments" : [ "Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002114" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_via_type_III_bouton_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002115", + "lbl" 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 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}, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002297" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002298" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_morphogenesis_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_maturation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002300" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_disappearance_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002301" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_regression_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002302" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_treated_by_substance" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002303" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_habitat" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002304" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002305" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002309" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stimulus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002313" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports_or_maintains_localization_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "xrefs" : [ { + "val" : "RO:0002314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : 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"http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_acquisition_of_features_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002321" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "colocalizes_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002326" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002327" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enables" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "xrefs" : [ { + "val" : "RO:0002328" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "functionally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "xrefs" : [ { + "val" : "RO:0002329" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_structure_that_is_capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "xrefs" : [ { + "val" : "RO:0002331" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "xrefs" : [ { + "val" : "RO:0002332" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_levels_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002333" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enabled_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002334" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002335" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002336" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "xrefs" : [ { + "val" : "RO:0002337" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_localization_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002338" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002339" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002340" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "imports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "xrefs" : [ { + "val" : "RO:0002341" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_along" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002342" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002343" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_growth_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002344" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' 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"http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "exports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002348", + "lbl" : "results in commitment to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002348" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. 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It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. 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"RO:0002445" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitized_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. 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We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "subject_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002463" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "target_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002469" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_nutrients_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002470" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "eats" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002471" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_eaten_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002473" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "composed_primarily_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "xrefs" : [ { + "val" : "RO:0002476" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/subsets/ro-causal.obo b/src/ontology/subsets/ro-causal.obo index 9472403f..87ecf23c 100644 --- a/src/ontology/subsets/ro-causal.obo +++ b/src/ontology/subsets/ro-causal.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-causal -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/src/ontology/subsets/ro-causal.owl b/src/ontology/subsets/ro-causal.owl index d6ac9788..bada75b7 100644 --- a/src/ontology/subsets/ro-causal.owl +++ b/src/ontology/subsets/ro-causal.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-causal.tsv b/src/ontology/subsets/ro-causal.tsv new file mode 100644 index 00000000..23e4cd33 --- /dev/null +++ b/src/ontology/subsets/ro-causal.tsv @@ -0,0 +1,51 @@ +?x ?label +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid1 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid18 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid22 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid26 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid33 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid37 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid40 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid5 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid52 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid58 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid61 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid64 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid67 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-chado.json b/src/ontology/subsets/ro-chado.json new file mode 100644 index 00000000..ed2616ac --- /dev/null +++ b/src/ontology/subsets/ro-chado.json @@ -0,0 +1,16507 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-chado.owl", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#versionInfo", + "val" : "2023-02-19" + } ], + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-19/subsets/ro-chado.owl" + }, + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease is realized in this disease course" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is realized in this shattering" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is realized in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is realized by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "realized_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realizes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease course realizes this disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation realizes this investigator role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this shattering realizes this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000060", + "lbl" : "obsolete preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occurs_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "site of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01003004", + "lbl" : "derives from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000078", + "lbl" : "curation status specification", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "lbl" : "obsolescence reason specification", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl" : "OBO foundry unique label", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002105", + "lbl" : "synapsed_via_type_Ib_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton." + }, + "comments" : [ "Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002106", + "lbl" : "synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002107", + "lbl" : "synapsed_via_type_II_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and 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"http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "lbl" : "derived by descent from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral_stucture_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "evolutionarily_descended_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "lbl" : "has derived by descendant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of derived by descent from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "lbl" : "serially homologous to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + }, + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9227-417X" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002171", + "lbl" : "mutually spatially disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "non-overlapping with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no parts with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX owl: \nPREFIX part_of: \nPREFIX mutually_spatially_disjoint_with: \nCONSTRUCT {\n part_of: a owl:ObjectProperty .\n [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?x ;\n owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?y\n ]\n ]\n}\nWHERE {\n ?x mutually_spatially_disjoint_with: ?y .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/RO_0002163" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002172", + "lbl" : "taxonomic class assertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002173", + "lbl" : "ambiguous for taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002174", + "lbl" : "dubious for taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T." + }, + "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" + }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002204", + "lbl" : "gene product of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "lbl" : "has gene product", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002214", + "lbl" : "has prototype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002217", + "lbl" : "obsolete actively participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" + }, + "comments" : [ "Obsoleted as the inverse property was obsoleted." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "agent in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002608" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002218", + "lbl" : "obsolete has active participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has agent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002500" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Allen" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ends with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "finished by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002245", + "lbl" : "over-expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002246", + "lbl" : "under-expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "lbl" : "defined by inverse", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002291", + "lbl" : "ubiquitously expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'expressed in'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002293", + "lbl" : "ubiquitously expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ubiquiotously expressed in" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002312", + "lbl" : "evolutionary variant of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002345", + "lbl" : "exports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002348", + "lbl" : "results in commitment to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002349", + "lbl" : "results in determination of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "lbl" : "member of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "is member of is a mereological relation between a item and a collection." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An organism that is a member of a population of organisms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is member of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "member part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "lbl" : "has member", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "lbl" : "input of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has input" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "lbl" : "output of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has output" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "lbl" : "formed as result of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002355", + "lbl" : "results in structural organization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002356", + "lbl" : "results in specification of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002374", + "lbl" : "derived from ancestral fusion of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" + }, + "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "has fused element" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002401", + "lbl" : "obsolete has indirect input", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002402", + "lbl" : "obsolete has direct output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "translation SubClassOf has_direct_output some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly produces" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002403", + "lbl" : "obsolete has indirect output", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002406", + "lbl" : "obsolete directly activates", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002629" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002408", + "lbl" : "obsolete directly inhibits", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002630" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002416", + "lbl" : "logical macro assertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002419", + "lbl" : "annotation property cardinality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002420", + "lbl" : "logical macro assertion on a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a class" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002421", + "lbl" : "logical macro assertion on a property", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a property" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002422", + "lbl" : "logical macro assertion on an object property", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "lbl" : "logical macro assertion on an annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002424", + "lbl" : "differs in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This is an exploratory relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002425", + "lbl" : "differs in attribute of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "lbl" : "differs in attribute", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000316" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0208" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "lbl" : "molecularly interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "binds" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "molecularly binds with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0915" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002437", + "lbl" : "biotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "interacts with on organism level" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/interactsWith" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002438", + "lbl" : "trophically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the partners are related via a feeding relationship." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "lbl" : "preys on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Baleen whale preys on krill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7134-3324" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of predation interaction with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preys upon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/preysUpon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.inaturalist.org/observations/2942824" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002440", + "lbl" : "symbiotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction in which the two organisms live together in more or less intimate association." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002441", + "lbl" : "commensually interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002442", + "lbl" : "mutualistically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "lbl" : "interacts with via parasite-host interaction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002444", + "lbl" : "parasite of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "direct parasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Pediculus humanus capitis parasite of human" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitizes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/parasitizes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002445", + "lbl" : "parasitized by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "directly parasitized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "semibiotically interacts with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Porifiera attaches to substrate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002447", + "lbl" : "phosphorylates", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "lbl" : "directly regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly decreases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly inhibits" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "lbl" : "directly positively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly increases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly activates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002451", + "lbl" : "transmitted by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a disease and organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "all dengue disease transmitted by some mosquito" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Add domain and range constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002452", + "lbl" : "has symptom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between a disease or an organism and a phenotype" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002453", + "lbl" : "host of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "lbl" : "has host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasHost" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002455", + "lbl" : "pollinates", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Bees pollinate Flowers" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/pollinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "lbl" : "pollinated by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has polinator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasPollinator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "lbl" : "acquires nutrients from", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002458", + "lbl" : "preyed upon by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of preys on" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has predator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of predation interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/HasPredator" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "lbl" : "is vector for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002460", + "lbl" : "has vector", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002461", + "lbl" : "partner in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002462", + "lbl" : "subject participant in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002464", + "lbl" : "helper property (not for use in curation)", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002465", + "lbl" : "is symbiosis", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002466", + "lbl" : "is commensalism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002467", + "lbl" : "is mutualism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002468", + "lbl" : "is parasitism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002472", + "lbl" : "is evidence for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002474", + "lbl" : "dispositional interpretation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002475", + "lbl" : "has no connections with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no connection with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002481", + "lbl" : "is kinase activity", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002482", + "lbl" : "is ubiquitination", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002483", + "lbl" : "inherited annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002484", + "lbl" : "curator guidance link", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "exists during" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/BFO_0000169" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002503", + "lbl" : "towards", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002504", + "lbl" : "always present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brain always_present_in_taxon 'Vertebrata'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "forelimb always_present_in_taxon Euarchontoglires" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "never lost in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002505", + "lbl" : "has intermediate", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has intermediate product" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002506", + "lbl" : "causal relation between entities", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002507", + "lbl" : "determined by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A coral reef environment is determined by a particular coral reef" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/24330602" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determined by (system to material entity)" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002508", + "lbl" : "determines", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of determined by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determines (material entity to system)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002509", + "lbl" : "determined by part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002510", + "lbl" : "transcribed from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is transcribed from y if and only if x is synthesized from template y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002511", + "lbl" : "transcribed to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of transcribed from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002512", + "lbl" : "ribosomal translation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002513", + "lbl" : "ribosomally translates to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ribosomal translation of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002514", + "lbl" : "sequentially related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are sequentially adjacent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002516", + "lbl" : "has start sequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002518", + "lbl" : "has end sequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ended by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002519", + "lbl" : "is end sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has end sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002520", + "lbl" : "is consecutive sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the SO paper, this was defined as an instance-type relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002521", + "lbl" : "is sequentially aligned with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "lbl" : "bounds sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002523", + "lbl" : "is bound by sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of bounds sequence of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "lbl" : "has subsequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contains" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "lbl" : "is subsequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has subsequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained by" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "lbl" : "overlaps sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002527", + "lbl" : "does not overlap sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "disconnected from" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "lbl" : "is upstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of downstream of sequence of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "lbl" : "is downstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002530", + "lbl" : "is immediately downstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002529" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002531", + "lbl" : "is immediately upstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of immediately downstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002535", + "lbl" : "temporal logical macro assertion on a class", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002536", + "lbl" : "measurement property has unit", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002537", + "lbl" : "has start time value", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002538", + "lbl" : "has end time value", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002539", + "lbl" : "start, days post fertilization", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002540", + "lbl" : "end, days post fertilization", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002541", + "lbl" : "start, years post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002542", + "lbl" : "end, years post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002543", + "lbl" : "start, months post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002544", + "lbl" : "end, months post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002545", + "lbl" : "month of gestation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002546", + "lbl" : "has developmental stage marker", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002547", + "lbl" : "start, days post coitum", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of coitum." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002548", + "lbl" : "end, days post coitum", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the end of the stage and the time of coitum." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002549", + "lbl" : "start, weeks post birth", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002550", + "lbl" : "end, weeks post birth", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002551", + "lbl" : "has skeleton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has supporting framework" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002552", + "lbl" : "results in ending of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002553", + "lbl" : "hyperparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "hyperparasitoid of" + }, { + "pred" : "hasRelatedSynonym", + "val" : "epiparasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://eol.org/schema/terms/hyperparasitoidOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Hyperparasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "lbl" : "hyperparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of hyperparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "has epiparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has hyperparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hyperparasitoidized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002555", + "lbl" : "allelopath of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Allelopathy" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/allelopathyYes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002556", + "lbl" : "pathogen of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002557", + "lbl" : "has pathogen", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002558", + "lbl" : "has evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of is evidence for" + }, + "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/25052702" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "lbl" : "causally influenced by", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influenced by (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002560", + "lbl" : "is asymmetric relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002561", + "lbl" : "is symmetric relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002562", + "lbl" : "is relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "lbl" : "interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "lbl" : "molecular interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002565", + "lbl" : "results in movement of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "lbl" : "causally influences", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "lbl" : "biomechanically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002568", + "lbl" : "has muscle antagonist", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Antagonist_(muscle)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002569", + "lbl" : "has branching part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of branching part of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "lbl" : "conduit for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "UBERON:cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002571", + "lbl" : "lumen of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:cjm" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002572", + "lbl" : "luminal space of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002573", + "lbl" : "has modifier", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between an attribute or a qualifier and another attribute." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002574", + "lbl" : "participates in a biotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002575", + "lbl" : "is direct form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002423", + "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "lbl" : "skeleton of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has skeleton" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "lbl" : "directly regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002579", + "lbl" : "is indirect form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002580", + "lbl" : "logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002581", + "lbl" : "is a defining property chain axiom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002583", + "lbl" : "existence starts at end of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002584", + "lbl" : "has part structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002585", + "lbl" : "results in closure of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002586", + "lbl" : "results in breakdown of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002587", + "lbl" : "results in synthesis of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002588", + "lbl" : "results in assembly of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002589", + "lbl" : "results in catabolism of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002590", + "lbl" : "results in disassembly of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002591", + "lbl" : "results in remodeling of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002592", + "lbl" : "results in organization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002593", + "lbl" : "existence ends at start of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002594", + "lbl" : "is relational form of a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "lbl" : "causal relation between material entity and a process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002596", + "lbl" : "capable of regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pyrethroid -> growth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "lbl" : "capable of negatively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "lbl" : "capable of positively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "renin -> arteriolar smooth muscle contraction" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002599", + "lbl" : "capable of inhibiting or preventing pathological process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pazopanib -> pathological angiogenesis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002600", + "lbl" : "capable of upregulating or causing pathological process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "benzene -> cancer [CHEBI]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "causes disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002601", + "lbl" : "logical macro assertion involving identity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A shortcut relationship that holds between two entities based on their identity criteria" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002602", + "lbl" : "in approximate one to one relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002603", + "lbl" : "is approximately equivalent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002604", + "lbl" : "is opposite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002605", + "lbl" : "is indistinguishable from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002606", + "lbl" : "is substance that treats", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002607", + "lbl" : "is marker for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be ceded to OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002608", + "lbl" : "process has causal agent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'causal agent in process'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002609", + "lbl" : "obsolete related via dependence to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002610", + "lbl" : "correlated with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Groups both positive and negative correlation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002611", + "lbl" : "evidential logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002612", + "lbl" : "axiom has evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002613", + "lbl" : "axiom contradicted by evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002614", + "lbl" : "is evidence with support from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." + }, + "comments" : [ "In the Gene Ontology association model, this corresponds to the With/From field" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002615", + "lbl" : "has model", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of is-model-of" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002616", + "lbl" : "related via evidence or inference to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002617", + "lbl" : "is representative IRI for equivalence set", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002618", + "lbl" : "visits", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/74" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002619", + "lbl" : "visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002622", + "lbl" : "visits flowers of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002623", + "lbl" : "has flowers visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002624", + "lbl" : "lays eggs in", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002625", + "lbl" : "has eggs laid in by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002626", + "lbl" : "kills", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://github.com/jhpoelen/eol-globi-data/issues/143" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002627", + "lbl" : "is killed by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "lbl" : "directly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002630", + "lbl" : "directly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002632", + "lbl" : "ectoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002633", + "lbl" : "has ectoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ectoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002634", + "lbl" : "endoparasite of", + "type" : "PROPERTY", + "meta" : { + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "lives inside of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002635", + "lbl" : "has endoparasite", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002636", + "lbl" : "mesoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002637", + "lbl" : "has mesoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of mesoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002638", + "lbl" : "intercellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002639", + "lbl" : "has intercellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intercellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002640", + "lbl" : "intracellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002641", + "lbl" : "has intracellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intracellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002801", + "lbl" : "co-roosts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Communal_roosting" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003000", + "lbl" : "produces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." + }, + "comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "lbl" : "produced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a produced_by b iff some process that occurs_in b has_output a." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003002", + "lbl" : "represses expression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003003", + "lbl" : "increases expression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "lbl" : "has role in modeling", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." + }, + "comments" : [ "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-1048-5019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is used to study" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "lbl" : "causes or contributes to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." + }, + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003303", + "lbl" : "causes condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "lbl" : "contributes to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "lbl" : "contributes to severity of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to expressivity of condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003306", + "lbl" : "contributes to frequency of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to penetrance of condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "lbl" : "ameliorates condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." + }, + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preventative for condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003308", + "lbl" : "correlated with condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003309", + "lbl" : "exacerbates condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003310", + "lbl" : "condition ameliorated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003311", + "lbl" : "condition exacerbated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004000", + "lbl" : "condition has genetic basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:38:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004001", + "lbl" : "has material basis in gain of function germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:20Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410295" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410296" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004002", + "lbl" : "has material basis in loss of function germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004003", + "lbl" : "has material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:54Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004004", + "lbl" : "has material basis in somatic mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:07Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004005", + "lbl" : "has major susceptibility factor", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:26Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004006", + "lbl" : "has partial material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:57Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004007", + "lbl" : "has primary input or output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004008", + "lbl" : "has primary output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", + "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004009", + "lbl" : "has primary input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", + "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:56Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004010", + "lbl" : "is genetic basis for condition", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:53:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004011", + "lbl" : "is causal gain of function germline mutation of in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : 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"http://purl.obolibrary.org/obo/RO_0004013", + "lbl" : "is causal germline mutation in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:56:40Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004014", + "lbl" : "is causal somatic mutation in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:57:07Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004015", + "lbl" : "is causal susceptibility factor for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + 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"http://purl.obolibrary.org/obo/RO_0004017", + "lbl" : "realizable has basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:01Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004018", + "lbl" : "is basis for realizable", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004019", + "lbl" : "disease has basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:26:47Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004020", + "lbl" : "disease has basis in dysfunction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in dysfunction of (disease to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:29:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004021", + "lbl" : "disease has basis in disruption of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:37:52Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004022", + "lbl" : "disease has basis in feature", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the 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It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:50:54Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004024", + "lbl" : "disease causes disruption of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:51:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004025", + "lbl" : "disease causes dysfunction of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes dysfunction of (disease to anatomical entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:58:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004026", + "lbl" : "disease has location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T04:06:02Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004027", + "lbl" : "disease has inflammation site", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:37:31Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004029", + "lbl" : "disease has feature", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:50:53Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "lbl" : "disease arises from alteration in structure", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "lbl" : "enables subfunction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-25T23:20:13Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "lbl" : "acts upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:30Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "lbl" : "acts upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:51Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "lbl" : "acts upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "lbl" : "acts upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004036", + "lbl" : "nominally disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004048", + "lbl" : "is directional form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:59:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004049", + "lbl" : "is positive form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:16Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004096", + "lbl" : "DEPRECATED inheres in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004097", + "lbl" : "DEPRECATED bearer of", + "type" : "PROPERTY", + "meta" : { + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007000", + "lbl" : "has driver", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007001", + "lbl" : "has disease driver", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008501", + "lbl" : "epiphyte of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Epiphyte" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008502", + "lbl" : "has epiphyte", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of epiphyte of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008503", + "lbl" : "kleptoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008504", + "lbl" : "kleptoparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of kleptoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008505", + "lbl" : "creates habitat for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008506", + "lbl" : "ecologically co-occurs with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008507", + "lbl" : "lays eggs on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008508", + "lbl" : "has eggs laid on by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of lays eggs on" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009001", + "lbl" : "has substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "muffin 'has substance added' some 'baking soda'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009002", + "lbl" : "has substance removed", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'egg white' 'has substance removed' some 'egg yolk'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009003", + "lbl" : "immersed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardines 'immersed in' some 'oil and mustard'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009004", + "lbl" : "has consumer", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardine has consumer some homo sapiens" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009005", + "lbl" : "has primary substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bread 'has primary substance added' some 'flour'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "lbl" : "realized in response to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "triggered by process", + "xrefs" : [ "RO:cjm" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : 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"receives synaptic input throughout", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:55:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013006", + "lbl" : "sends synaptic output throughout", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:57:27Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013007", + "lbl" : "has sensory dendrite in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has sensory dendrite location" + }, { + "pred" : "hasExactSynonym", + "val" : "has sensory terminal in" + }, { + "pred" : "hasExactSynonym", + "val" : "has sensory terminal location" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-20T12:10:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013008", + "lbl" : "receives synaptic input from neuron", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-05-26T08:40:18Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013009", + "lbl" : "sends synaptic output to cell", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." + }, + "comments" : [ "Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-05-26T08:41:07Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0014001", + "lbl" : "disease has infectious agent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015001", + "lbl" : "has exemplar data", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-5260-9315" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is not meant to capture the relation between occurrents and data." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015002", + "lbl" : "exemplar data of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-5260-9315" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015003", + "lbl" : "subcluster of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a group and another group it is part of but does not fully constitute." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7258-9596" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context." + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015006", + "lbl" : "different in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015007", + "lbl" : "increased in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "lbl" : "decreased in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015009", + "lbl" : "similar in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "lbl" : "has relative magnitude", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015011", + "lbl" : "has cross section", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015012", + "lbl" : "reciprocal of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015015", + "lbl" : "has high plasma membrane amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "lbl" : "has low plasma membrane amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016001", + "lbl" : "has phenotype or disease", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016002", + "lbl" : "has disease", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:44Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016004", + "lbl" : "has exposure medium", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000083" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-12-14T20:41:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7463-6306" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017001", + "lbl" : "device utilizes material", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "utilizes" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A diagnostic testing device utilizes a specimen." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-2620-0345" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-11-08T12:00:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018001", + "lbl" : "is myristoyltransferase activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Helper relation for OWL definition of RO:0018002 myristoylates" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018002", + "lbl" : "myristoylates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/conformsTo", + "val" : "http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018003", + "lbl" : "myristoylated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of myristoylates" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018027", + "lbl" : "is agonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P3772" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018028", + "lbl" : "is inverse agonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + 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"chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002409" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002403", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002402" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002553", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002444", "http://purl.obolibrary.org/obo/RO_0002444" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002554", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002445", "http://purl.obolibrary.org/obo/RO_0002445" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000062" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/RO_0002082" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000063" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002509", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002507", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002205", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002511", "http://purl.obolibrary.org/obo/RO_0002513" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002204", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002512", "http://purl.obolibrary.org/obo/RO_0002510" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002526", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002524", "http://purl.obolibrary.org/obo/RO_0002525" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002583", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002593", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004024", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013002", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013003", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013003", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013007", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0015001", "http://purl.obolibrary.org/obo/RO_0015003" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/subsets/ro-chado.obo b/src/ontology/subsets/ro-chado.obo index 300fa699..6dedea73 100644 --- a/src/ontology/subsets/ro-chado.obo +++ b/src/ontology/subsets/ro-chado.obo @@ -5,21 +5,6 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 60 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 310 Logical Axioms: 68] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 0 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 45 Logical Axioms: 10] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 3 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 104 Logical Axioms: 26] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] default-namespace: relationship ontology: ro/subsets/ro-chado.obo property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string @@ -91,6 +76,11 @@ id: BFO:0000067 name: contains_process def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +[Typedef] +id: ENVO:01003004 +name: derives_from_part_of +def: "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." [] + [Typedef] id: RO:0000052 name: characteristic_of diff --git a/src/ontology/subsets/ro-chado.obo.tmp b/src/ontology/subsets/ro-chado.obo.tmp deleted file mode 100644 index 1b4b78ac..00000000 --- a/src/ontology/subsets/ro-chado.obo.tmp +++ /dev/null @@ -1,4352 +0,0 @@ -format-version: 1.2 -subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" -subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" -subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" -subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" -subsetdef: ro-eco "" -subsetdef: RO:0002259 "" -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 60 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 310 Logical Axioms: 68] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 0 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 45 Logical Axioms: 10] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 3 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 104 Logical Axioms: 26] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] -ontology: ro/subsets/ro-chado.obo -property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "OBO Relations Ontology" xsd:string -property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ -property_value: http://xmlns.com/foaf/0.1/homepage " https://github.com/oborel/obo-relations/" xsd:anyURI -property_value: owl:versionInfo "2023-02-19" xsd:string -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (has member)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: ()\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\n) - -[Typedef] -id: BFO:0000050 -name: part of -def: "a core relation that holds between a part and its whole" [] -is_transitive: true -is_a: RO:0002131 ! overlaps -inverse_of: BFO:0000051 ! has part - -[Typedef] -id: BFO:0000051 -name: has part -def: "a core relation that holds between a whole and its part" [] -is_transitive: true -is_a: RO:0002131 ! overlaps - -[Typedef] -id: BFO:0000054 -name: realized in -inverse_of: BFO:0000055 ! realizes - -[Typedef] -id: BFO:0000055 -name: realizes - -[Typedef] -id: BFO:0000060 -name: obsolete preceded by -is_transitive: true -is_obsolete: true - -[Typedef] -id: BFO:0000062 -name: preceded by -def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -holds_over_chain: BFO:0000050 BFO:0000062 -holds_over_chain: RO:0002091 BFO:0000062 -holds_over_chain: RO:0002092 BFO:0000062 -is_transitive: true -is_a: RO:0002086 ! ends after -inverse_of: BFO:0000063 ! precedes - -[Typedef] -id: BFO:0000063 -name: precedes -def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -holds_over_chain: BFO:0000050 BFO:0000063 -holds_over_chain: RO:0002092 BFO:0000063 -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: BFO:0000066 -name: occurs in -def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -holds_over_chain: BFO:0000050 BFO:0000066 -inverse_of: BFO:0000067 ! contains process -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: BFO:0000067 -name: contains process -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] - -[Typedef] -id: RO:0000052 -name: characteristic of -def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] -is_functional: true -is_a: RO:0002314 ! characteristic of part of -inverse_of: RO:0000053 ! has characteristic - -[Typedef] -id: RO:0000053 -name: has characteristic -def: "Inverse of characteristic_of" [] -is_inverse_functional: true - -[Typedef] -id: RO:0000056 -name: participates in -def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] -inverse_of: RO:0000057 ! has participant - -[Typedef] -id: RO:0000057 -name: has participant -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -holds_over_chain: BFO:0000051 RO:0000057 - -[Typedef] -id: RO:0000058 -name: is concretized as -def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] -inverse_of: RO:0000059 ! concretizes - -[Typedef] -id: RO:0000059 -name: concretizes -def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] - -[Typedef] -id: RO:0000079 -name: function of -def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] -is_a: RO:0000052 ! characteristic of -inverse_of: RO:0000085 ! has function - -[Typedef] -id: RO:0000080 -name: quality of -def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] -is_a: RO:0000052 ! characteristic of -inverse_of: RO:0000086 ! has quality - -[Typedef] -id: RO:0000081 -name: role of -def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] -is_a: RO:0000052 ! characteristic of -inverse_of: RO:0000087 ! has role - -[Typedef] -id: RO:0000085 -name: has function -def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -is_a: RO:0000053 ! has characteristic - -[Typedef] -id: RO:0000086 -name: has quality -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -is_a: RO:0000053 ! has characteristic - -[Typedef] -id: RO:0000087 -name: has role -def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -is_a: RO:0000053 ! has characteristic - -[Typedef] -id: RO:0000091 -name: has disposition -def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] -is_a: RO:0000053 ! has characteristic -inverse_of: RO:0000092 ! disposition of - -[Typedef] -id: RO:0000092 -name: disposition of -def: "inverse of has disposition" [] -is_a: RO:0000052 ! characteristic of - -[Typedef] -id: RO:0000300 -name: obsolete in neural circuit with -def: "OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons." [] -is_transitive: true -is_obsolete: true - -[Typedef] -id: RO:0000301 -name: obsolete upstream in neural circuit with -def: "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first." [] -is_transitive: true -is_obsolete: true - -[Typedef] -id: RO:0000302 -name: obsolete downstream in neural circuit with -def: "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first." [] -is_transitive: true -is_obsolete: true - -[Typedef] -id: RO:0001000 -name: derives from -def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] -inverse_of: RO:0001001 ! derives into - -[Typedef] -id: RO:0001001 -name: derives into -def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] - -[Typedef] -id: RO:0001015 -name: location of -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -is_transitive: true -inverse_of: RO:0001025 ! located in - -[Typedef] -id: RO:0001018 -name: contained in -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains - -[Typedef] -id: RO:0001019 -name: contains - -[Typedef] -id: RO:0001020 -name: is allergic trigger for -def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] -is_a: RO:0003302 ! causes or contributes to condition -inverse_of: RO:0001022 ! has allergic trigger - -[Typedef] -id: RO:0001021 -name: is autoimmune trigger for -def: "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] -is_a: RO:0003302 ! causes or contributes to condition -inverse_of: RO:0001023 ! has autoimmune trigger - -[Typedef] -id: RO:0001022 -name: has allergic trigger -def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] -is_a: RO:0003302 ! causes or contributes to condition - -[Typedef] -id: RO:0001023 -name: has autoimmune trigger -def: "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." [] -is_a: RO:0003302 ! causes or contributes to condition - -[Typedef] -id: RO:0001025 -name: located in -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -is_transitive: true -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002000 -name: 2D boundary of -def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -is_a: RO:0002323 ! mereotopologically related to -inverse_of: RO:0002002 ! has 2D boundary - -[Typedef] -id: RO:0002001 -name: aligned with -is_transitive: true - -[Typedef] -id: RO:0002002 -name: has 2D boundary -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002003 -name: electrically_synapsed_to -def: "A relation that holds between two neurons that are electrically coupled via gap junctions." [] -is_a: RO:0002170 ! connected to - -[Typedef] -id: RO:0002004 -name: tracheates -def: "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." [] -is_a: RO:0001018 ! contained in - -[Typedef] -id: RO:0002005 -name: innervated_by -inverse_of: RO:0002134 ! innervates - -[Typedef] -id: RO:0002006 -name: has synaptic terminal of -is_a: RO:0002131 ! overlaps -inverse_of: RO:0002130 ! has synaptic terminal in - -[Typedef] -id: RO:0002007 -name: bounding layer of -def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] -is_a: BFO:0000050 ! part of - -[Typedef] -id: RO:0002008 -name: coincident with -def: "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002009 -name: cell expresses -def: "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." [] -is_a: RO:0002292 ! expresses - -[Typedef] -id: RO:0002010 -name: regulates in other organism -def: "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." [] -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002011 -name: regulates transport of -def: "A relationship that holds between a process that regulates a transport process and the entity transported by that process." [] -holds_over_chain: RO:0002211 RO:0002313 - -[Typedef] -id: RO:0002012 -name: occurrent part of -def: "A part of relation that applies only between occurrents." [] -is_a: BFO:0000050 ! part of -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002016 -name: has necessary component activity -is_a: RO:0002017 ! has component activity -is_a: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002017 -name: has component activity -is_a: RO:0002018 ! has component process - -[Typedef] -id: RO:0002018 -name: has component process -def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -is_a: RO:0002180 ! has component - -[Typedef] -id: RO:0002019 -name: has ligand -def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] -is_a: RO:0002233 ! has input - -[Typedef] -id: RO:0002020 -name: transports -def: "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." [] -is_a: RO:0002313 ! transports or maintains localization of - -[Typedef] -id: RO:0002021 -name: occurs across -def: "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." [] -is_a: RO:0002479 ! has part that occurs in - -[Typedef] -id: RO:0002022 -name: directly regulated by -is_a: RO:0002334 ! regulated by -inverse_of: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002023 -name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002630 ! directly negatively regulates - -[Typedef] -id: RO:0002024 -name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002629 ! directly positively regulates - -[Typedef] -id: RO:0002025 -name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] -is_functional: true -is_a: RO:0002017 ! has component activity - -[Typedef] -id: RO:0002026 -name: in register with -def: "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software." [GOC:dos] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002081 -name: before or simultaneous with -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002082 -name: simultaneous with -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with - -[Typedef] -id: RO:0002083 -name: before -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with - -[Typedef] -id: RO:0002084 -name: during which ends -is_a: RO:0002222 ! temporally related to -inverse_of: RO:0002093 ! ends during - -[Typedef] -id: RO:0002085 -name: encompasses -is_transitive: true -is_a: RO:0002088 ! during which starts -inverse_of: RO:0002092 ! happens during - -[Typedef] -id: RO:0002086 -name: ends after -holds_over_chain: RO:0002093 BFO:0000062 -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002087 -name: immediately preceded by -holds_over_chain: RO:0002224 RO:0002230 -is_a: BFO:0000062 ! preceded by -inverse_of: RO:0002090 ! immediately precedes - -[Typedef] -id: RO:0002088 -name: during which starts -is_a: RO:0002222 ! temporally related to -inverse_of: RO:0002091 ! starts during - -[Typedef] -id: RO:0002089 -name: starts before -holds_over_chain: RO:0002091 BFO:0000060 -is_transitive: true -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002090 -name: immediately precedes -holds_over_chain: RO:0002230 RO:0002224 -is_a: BFO:0000063 ! precedes - -[Typedef] -id: RO:0002091 -name: starts during -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002092 -name: happens during -is_transitive: true -is_a: RO:0002091 ! starts during -is_a: RO:0002093 ! ends during - -[Typedef] -id: RO:0002093 -name: ends during -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002100 -name: has soma location -def: "Relation between a neuron and an anatomical structure that its soma is part of." [] -is_a: RO:0002131 ! overlaps -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002101 -name: fasciculates with -def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -is_a: RO:0002131 ! overlaps -inverse_of: RO:0002132 ! has fasciculating neuron projection - -[Typedef] -id: RO:0002102 -name: axon synapses in -def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -is_a: RO:0002113 ! has presynaptic terminal in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002103 -name: synapsed by -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -is_a: RO:0002485 ! receives input from -inverse_of: RO:0002120 ! synapsed to - -[Typedef] -id: RO:0002104 -name: has plasma membrane part -def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002105 -name: synapsed_via_type_Ib_bouton_to -def: "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton." [] -is_a: RO:0002120 ! synapsed to -inverse_of: RO:0002109 ! synapsed_by_via_type_Ib_bouton - -[Typedef] -id: RO:0002106 -name: synapsed_via_type_Is_bouton_to -def: "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." [] -is_a: RO:0002120 ! synapsed to -inverse_of: RO:0002112 ! synapsed_by_via_type_Is_bouton - -[Typedef] -id: RO:0002107 -name: synapsed_via_type_II_bouton_to -def: "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." [] -is_a: RO:0002120 ! synapsed to -inverse_of: RO:0002108 ! synapsed_by_via_type_II_bouton - -[Typedef] -id: RO:0002108 -name: synapsed_by_via_type_II_bouton -def: "Relation between a muscle and a motor neuron that synapses to it via a type II bouton." [] -is_a: RO:0002103 ! synapsed by - -[Typedef] -id: RO:0002109 -name: synapsed_by_via_type_Ib_bouton -def: "Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton." [] -is_a: RO:0002103 ! synapsed by - -[Typedef] -id: RO:0002110 -name: has postsynaptic terminal in -def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -is_a: RO:0002130 ! has synaptic terminal in -inverse_of: RO:0002113 ! has presynaptic terminal in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002111 -name: releases neurotransmitter - -[Typedef] -id: RO:0002112 -name: synapsed_by_via_type_Is_bouton -def: "Relation between a muscle and a motor neuron that synapses to it via a type Is bouton." [] -is_a: RO:0002103 ! synapsed by - -[Typedef] -id: RO:0002113 -name: has presynaptic terminal in -def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -is_a: RO:0002130 ! has synaptic terminal in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002114 -name: synapsed_via_type_III_bouton_to -def: "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." [] -is_a: RO:0002120 ! synapsed to -inverse_of: RO:0002115 ! synapsed_by_via_type_III_bouton - -[Typedef] -id: RO:0002115 -name: synapsed_by_via_type_III_bouton -def: "Relation between a muscle and a motor neuron that synapses to it via a type III bouton.\n" [] -is_a: RO:0002103 ! synapsed by - -[Typedef] -id: RO:0002120 -name: synapsed to -def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] -is_a: RO:0002486 ! sends output to - -[Typedef] -id: RO:0002121 -name: dendrite synapsed in -def: "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n " [] -is_a: RO:0002110 ! has postsynaptic terminal in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002130 -name: has synaptic terminal in -def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -is_a: RO:0002131 ! overlaps -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002131 -name: overlaps -def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] -holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: BFO:0000051 RO:0002131 -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002132 -name: has fasciculating neuron projection -def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002134 -name: innervates -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002150 -name: continuous with -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002151 -name: partially overlaps -def: "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" [] -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002156 -name: derived by descent from -def: "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." [] -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to -inverse_of: RO:0002157 ! has derived by descendant - -[Typedef] -id: RO:0002157 -name: has derived by descendant -def: "inverse of derived by descent from" [] -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: RO:0002158 -name: shares ancestor with -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -holds_over_chain: RO:0002156 RO:0002157 -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: RO:0002159 -name: serially homologous to -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: RO:0002160 -name: only in taxon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -is_a: RO:0002162 ! in taxon - -[Typedef] -id: RO:0002162 -name: in taxon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -holds_over_chain: BFO:0000050 RO:0002162 -holds_over_chain: BFO:0000051 RO:0002162 -holds_over_chain: RO:0002202 RO:0002162 -holds_over_chain: RO:0002206 RO:0002162 -holds_over_chain: RO:0002214 RO:0002162 -holds_over_chain: RO:0002215 RO:0002162 -holds_over_chain: RO:0002225 RO:0002162 -holds_over_chain: RO:0002254 RO:0002162 -holds_over_chain: RO:0002295 RO:0002162 -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: RO:0002163 -name: spatially disjoint from -def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002170 -name: connected to -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002176 -name: connects -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002177 -name: attached to part of -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: RO:0002178 -name: supplies -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -is_a: RO:0002170 ! connected to - -[Typedef] -id: RO:0002179 -name: drains -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -is_a: RO:0002170 ! connected to - -[Typedef] -id: RO:0002180 -name: has component -def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002200 -name: has phenotype -def: "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." [] -is_a: RO:0016001 ! has phenotype or disease -inverse_of: RO:0002201 ! phenotype of - -[Typedef] -id: RO:0002201 -name: phenotype of -def: "inverse of has phenotype" [] -is_functional: true - -[Typedef] -id: RO:0002202 -name: develops from -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -is_transitive: true -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002203 ! develops into - -[Typedef] -id: RO:0002203 -name: develops into -def: "inverse of develops from" [] -is_transitive: true -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002387 ! has potential to develop into -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: RO:0002204 -name: gene product of -def: "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" [] -holds_over_chain: RO:0002512 RO:0002510 -is_a: RO:0002330 ! genomically related to -inverse_of: RO:0002205 ! has gene product - -[Typedef] -id: RO:0002205 -name: has gene product -def: "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" [] -holds_over_chain: RO:0002511 RO:0002513 -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: RO:0002206 -name: expressed in -def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -is_a: RO:0002330 ! genomically related to -inverse_of: RO:0002292 ! expresses -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002207 -name: directly develops from -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] -synonym: "has developmental precursor" EXACT [] -is_a: RO:0002202 ! develops from -inverse_of: RO:0002210 ! directly develops into - -[Typedef] -id: RO:0002208 -name: parasitoid of -def: "A parasite that kills or sterilizes its host" [] -is_a: RO:0002444 ! parasite of -inverse_of: RO:0002209 ! has parasitoid - -[Typedef] -id: RO:0002209 -name: has parasitoid -def: "inverse of parasitoid of" [] -is_a: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0002210 -name: directly develops into -def: "inverse of directly develops from" [] -is_a: RO:0002203 ! develops into - -[Typedef] -id: RO:0002211 -name: regulates -def: "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." [] -holds_over_chain: RO:0002230 RO:0002211 -holds_over_chain: RO:0002578 RO:0002578 -is_transitive: true -is_a: RO:0002411 ! causally upstream of -inverse_of: RO:0002334 ! regulated by -transitive_over: RO:0002025 ! has effector activity - -[Typedef] -id: RO:0002212 -name: negatively regulates -def: "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." [] -holds_over_chain: RO:0002230 RO:0002212 -is_a: RO:0002211 ! regulates -is_a: RO:0002305 ! causally upstream of, negative effect -inverse_of: RO:0002335 ! negatively regulated by - -[Typedef] -id: RO:0002213 -name: positively regulates -def: "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." [] -holds_over_chain: RO:0002212 RO:0002212 -holds_over_chain: RO:0002230 RO:0002213 -is_transitive: true -is_a: RO:0002211 ! regulates -is_a: RO:0002304 ! causally upstream of, positive effect -inverse_of: RO:0002336 ! positively regulated by - -[Typedef] -id: RO:0002214 -name: has prototype -def: "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." [] - -[Typedef] -id: RO:0002215 -name: capable of -def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] -is_a: RO:0002216 ! capable of part of - -[Typedef] -id: RO:0002216 -name: capable of part of -def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002217 -name: obsolete actively participates in -def: "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" [] -is_obsolete: true -replaced_by: RO:0002608 - -[Typedef] -id: RO:0002218 -name: obsolete has active participant -def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" [] -is_obsolete: true -replaced_by: RO:0002500 - -[Typedef] -id: RO:0002219 -name: surrounded by -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -is_a: RO:0002220 ! adjacent to -inverse_of: RO:0002221 ! surrounds - -[Typedef] -id: RO:0002220 -name: adjacent to -def: "x adjacent to y if and only if x and y share a boundary." [] -is_a: RO:0002163 ! spatially disjoint from - -[Typedef] -id: RO:0002221 -name: surrounds -def: "inverse of surrounded by" [] -is_a: RO:0002220 ! adjacent to - -[Typedef] -id: RO:0002222 -name: temporally related to - -[Typedef] -id: RO:0002223 -name: starts -def: "inverse of starts with" [] -is_a: BFO:0000050 ! part of -is_a: RO:0002222 ! temporally related to -inverse_of: RO:0002224 ! starts with - -[Typedef] -id: RO:0002224 -name: starts with -def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -is_transitive: true -is_a: BFO:0000051 ! has part -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002225 -name: develops from part of -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -holds_over_chain: RO:0002207 BFO:0000050 -is_a: RO:0002202 ! develops from - -[Typedef] -id: RO:0002226 -name: develops in -def: "x develops_in y if x is located in y whilst x is developing" [] -holds_over_chain: RO:0002207 RO:0001025 -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: RO:0002227 -name: obligate parasite of -def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] -is_a: RO:0002444 ! parasite of - -[Typedef] -id: RO:0002228 -name: facultative parasite of -def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] -is_a: RO:0002444 ! parasite of - -[Typedef] -id: RO:0002229 -name: ends -def: "inverse of ends with" [] -is_a: BFO:0000050 ! part of -is_a: RO:0002222 ! temporally related to -inverse_of: RO:0002230 ! ends with - -[Typedef] -id: RO:0002230 -name: ends with -def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] -is_transitive: true -is_a: BFO:0000051 ! has part -is_a: RO:0002222 ! temporally related to - -[Typedef] -id: RO:0002231 -name: has start location -def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] -holds_over_chain: RO:0002224 BFO:0000066 -is_a: RO:0002479 ! has part that occurs in - -[Typedef] -id: RO:0002232 -name: has end location -def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] -holds_over_chain: RO:0002230 BFO:0000066 -is_a: RO:0002479 ! has part that occurs in - -[Typedef] -id: RO:0002233 -name: has input -def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] -holds_over_chain: RO:0002224 RO:0002233 -is_a: RO:0000057 ! has participant -inverse_of: RO:0002352 ! input of - -[Typedef] -id: RO:0002234 -name: has output -def: "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." [] -holds_over_chain: RO:0002230 RO:0002234 -is_a: RO:0000057 ! has participant -inverse_of: RO:0002353 ! output of - -[Typedef] -id: RO:0002235 -name: stem parasite of -def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] -is_a: RO:0002444 ! parasite of - -[Typedef] -id: RO:0002236 -name: root parasite of -def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] -is_a: RO:0002444 ! parasite of - -[Typedef] -id: RO:0002237 -name: hemiparasite of -def: "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." [] -is_a: RO:0002444 ! parasite of - -[Typedef] -id: RO:0002238 -name: has component participant -def: "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." [] -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0002240 -name: has exposure receptor -def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] -is_a: RO:0002244 ! related via exposure to - -[Typedef] -id: RO:0002241 -name: has exposure stressor -def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] -is_a: RO:0002309 ! has exposure stimulus - -[Typedef] -id: RO:0002242 -name: has exposure route -def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] -is_a: RO:0002244 ! related via exposure to - -[Typedef] -id: RO:0002243 -name: has exposure transport path -def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] -is_a: RO:0002244 ! related via exposure to - -[Typedef] -id: RO:0002244 -name: related via exposure to -def: "Any relationship between an exposure event or process and any other entity." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002245 -name: over-expressed in -def: "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." [] -is_a: RO:0002206 ! expressed in - -[Typedef] -id: RO:0002246 -name: under-expressed in -def: "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." [] -is_a: RO:0002206 ! expressed in - -[Typedef] -id: RO:0002248 -name: has active ingredient -def: "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." [] -synonym: "has active pharmaceutical ingredient" RELATED [] -synonym: "has active substance" EXACT [] -is_a: BFO:0000051 ! has part -inverse_of: RO:0002249 ! active ingredient in - -[Typedef] -id: RO:0002249 -name: active ingredient in -def: "inverse of has active ingredient" [] -is_a: BFO:0000050 ! part of - -[Typedef] -id: RO:0002252 -name: connecting branch of -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -is_a: RO:0002170 ! connected to -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: RO:0002253 -name: has connecting branch -def: "inverse of connecting branch of" [] -is_a: RO:0002375 ! in branching relationship with - -[Typedef] -id: RO:0002254 -name: has developmental contribution from -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -holds_over_chain: BFO:0000051 RO:0002202 -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - -[Typedef] -id: RO:0002255 -name: developmentally contributes to -def: "inverse of has developmental contribution from" [] -holds_over_chain: RO:0002203 BFO:0000050 -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002385 ! has potential to developmentally contribute to - -[Typedef] -id: RO:0002256 -name: developmentally induced by -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: RO:0002257 -name: developmentally induces -def: "Inverse of developmentally induced by" [] -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002386 ! has potential to developmentally induce - -[Typedef] -id: RO:0002258 -name: developmentally preceded by -def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] -is_a: RO:0002324 ! developmentally related to -inverse_of: RO:0002286 ! developmentally succeeded by - -[Typedef] -id: RO:0002260 -name: has biological role -def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] -is_a: RO:0000087 ! has role - -[Typedef] -id: RO:0002261 -name: has application role -def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] -is_a: RO:0000087 ! has role - -[Typedef] -id: RO:0002262 -name: has chemical role -def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] -is_a: RO:0000087 ! has role - -[Typedef] -id: RO:0002263 -name: acts upstream of -def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] -holds_over_chain: RO:0002327 RO:0002411 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0002264 -name: acts upstream of or within -def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] -synonym: "affects" RELATED [] -holds_over_chain: RO:0002327 RO:0002418 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002285 -name: developmentally replaces -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: RO:0002286 -name: developmentally succeeded by -def: "Inverse of developmentally preceded by" [] -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: RO:0002287 -name: part of developmental precursor of -holds_over_chain: BFO:0000050 RO:0002210 -is_a: RO:0002286 ! developmentally succeeded by - -[Typedef] -id: RO:0002291 -name: ubiquitously expressed in -def: "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" [] -is_a: RO:0002206 ! expressed in -inverse_of: RO:0002293 ! ubiquitously expresses - -[Typedef] -id: RO:0002292 -name: expresses -def: "Inverse of 'expressed in'" [] -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: RO:0002293 -name: ubiquitously expresses -def: "inverse of ubiquiotously expressed in" [] -is_a: RO:0002292 ! expresses - -[Typedef] -id: RO:0002295 -name: results in developmental progression of -def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] -is_a: RO:0002324 ! developmentally related to - -[Typedef] -id: RO:0002296 -name: results in development of -def: "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." [] -is_a: RO:0002295 ! results in developmental progression of -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002297 -name: results in formation of -is_a: RO:0002234 ! has output -is_a: RO:0002295 ! results in developmental progression of -inverse_of: RO:0002354 ! formed as result of - -[Typedef] -id: RO:0002298 -name: results in morphogenesis of -def: "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." [] -is_a: RO:0002295 ! results in developmental progression of -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002299 -name: results in maturation of -def: "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." [] -is_a: RO:0002295 ! results in developmental progression of -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002300 -name: results in disappearance of -is_a: RO:0002552 ! results in ending of - -[Typedef] -id: RO:0002301 -name: results in developmental regression of -is_a: RO:0002552 ! results in ending of - -[Typedef] -id: RO:0002302 -name: is treated by substance -def: "Inverse of 'is substance that treats'" [] -is_a: RO:0002410 ! causally related to -inverse_of: RO:0002606 ! is substance that treats - -[Typedef] -id: RO:0002303 -name: has habitat -def: "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." [] -is_a: RO:0002321 ! ecologically related to - -[Typedef] -id: RO:0002304 -name: causally upstream of, positive effect -def: "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." [] -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004047 ! causally upstream of or within, positive effect - -[Typedef] -id: RO:0002305 -name: causally upstream of, negative effect -def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] -is_a: RO:0002411 ! causally upstream of -is_a: RO:0004046 ! causally upstream of or within, negative effect - -[Typedef] -id: RO:0002309 -name: has exposure stimulus -def: "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." [] -is_a: RO:0002244 ! related via exposure to - -[Typedef] -id: RO:0002312 -name: evolutionary variant of -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: RO:0002313 -name: transports or maintains localization of -def: "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." [] -is_a: RO:0002337 ! related via localization to -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002314 -name: characteristic of part of -def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002502 ! depends on -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002315 -name: results in acquisition of features of -def: "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" [] -is_a: RO:0002295 ! results in developmental progression of -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002320 -name: evolutionarily related to -def: "A relationship that holds via some environmental process" [] - -[Typedef] -id: RO:0002321 -name: ecologically related to -def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] - -[Typedef] -id: RO:0002322 -name: confers advantage in -is_a: RO:0002321 ! ecologically related to - -[Typedef] -id: RO:0002323 -name: mereotopologically related to -def: "A mereological relationship or a topological relationship" [] - -[Typedef] -id: RO:0002324 -name: developmentally related to -def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] - -[Typedef] -id: RO:0002325 -name: colocalizes with -def: "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002326 -name: contributes to -is_a: RO:0002216 ! capable of part of -is_a: RO:0002329 ! part of structure that is capable of - -[Typedef] -id: RO:0002327 -name: enables -def: "c enables p iff c is capable of p and c acts to execute p." [] -is_a: RO:0002215 ! capable of -inverse_of: RO:0002333 ! enabled by -transitive_over: BFO:0000051 ! has part -transitive_over: RO:0002017 ! has component activity - -[Typedef] -id: RO:0002328 -name: functionally related to -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] - -[Typedef] -id: RO:0002329 -name: part of structure that is capable of -def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002330 -name: genomically related to -def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] - -[Typedef] -id: RO:0002331 -name: involved in -def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -holds_over_chain: RO:0002327 BFO:0000050 -is_a: RO:0000056 ! participates in -is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002332 -name: regulates levels of -def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002333 -name: enabled by -def: "inverse of enables" [] -is_a: RO:0000057 ! has participant -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002334 -name: regulated by -def: "inverse of regulates" [] -is_transitive: true -is_a: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002335 -name: negatively regulated by -def: "inverse of negatively regulates" [] -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002336 -name: positively regulated by -def: "inverse of positively regulates" [] -is_a: RO:0002334 ! regulated by - -[Typedef] -id: RO:0002337 -name: related via localization to -def: "A relationship that holds via some process of localization" [] - -[Typedef] -id: RO:0002338 -name: has target start location -def: "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." [] -is_a: RO:0002344 ! results in transport to from or in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002339 -name: has target end location -def: "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." [] -is_a: RO:0002344 ! results in transport to from or in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002340 -name: imports -def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." [] -is_a: RO:0002020 ! transports - -[Typedef] -id: RO:0002341 -name: results in transport along -def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] -is_a: RO:0002337 ! related via localization to - -[Typedef] -id: RO:0002342 -name: results in transport across -def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] -is_a: RO:0002021 ! occurs across -is_a: RO:0002344 ! results in transport to from or in - -[Typedef] -id: RO:0002343 -name: results in growth of -is_a: RO:0002295 ! results in developmental progression of -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002344 -name: results in transport to from or in -is_a: RO:0002337 ! related via localization to - -[Typedef] -id: RO:0002345 -name: exports -def: "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." [] -is_a: RO:0002020 ! transports - -[Typedef] -id: RO:0002348 -name: results in commitment to -def: "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." [] -is_a: RO:0002295 ! results in developmental progression of - -[Typedef] -id: RO:0002349 -name: results in determination of -def: "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment." [] -is_a: RO:0002295 ! results in developmental progression of - -[Typedef] -id: RO:0002350 -name: member of -def: "is member of is a mereological relation between a item and a collection." [] -is_a: BFO:0000050 ! part of -inverse_of: RO:0002351 ! has member - -[Typedef] -id: RO:0002351 -name: has member -def: "has member is a mereological relation between a collection and an item." [] -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002352 -name: input of -def: "inverse of has input" [] -is_a: RO:0000056 ! participates in -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002353 -name: output of -def: "inverse of has output" [] -is_a: RO:0000056 ! participates in -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002354 -name: formed as result of -is_a: RO:0002353 ! output of - -[Typedef] -id: RO:0002355 -name: results in structural organization of -def: "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." [] -is_a: RO:0002295 ! results in developmental progression of -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002356 -name: results in specification of -def: "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " [] -is_a: RO:0002295 ! results in developmental progression of - -[Typedef] -id: RO:0002357 -name: results in developmental induction of -def: "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." [] -is_a: RO:0002295 ! results in developmental progression of - -[Typedef] -id: RO:0002360 -name: has dendrite location -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002371 -name: attached to -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -is_symmetric: true -is_a: RO:0002170 ! connected to -is_a: RO:0002177 ! attached to part of - -[Typedef] -id: RO:0002372 -name: has muscle origin -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -is_a: RO:0002371 ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: RO:0002373 -name: has muscle insertion -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -is_a: RO:0002371 ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: RO:0002374 -name: derived from ancestral fusion of -def: "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" [] -synonym: "has fused element" BROAD [] -is_a: RO:0002156 ! derived by descent from - -[Typedef] -id: RO:0002375 -name: in branching relationship with -def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: RO:0002376 -name: tributary of -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -is_a: RO:0002170 ! connected to -is_a: RO:0002375 ! in branching relationship with - -[Typedef] -id: RO:0002377 -name: distributary of -def: "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" [] -is_a: RO:0002170 ! connected to -is_a: RO:0002375 ! in branching relationship with - -[Typedef] -id: RO:0002378 -name: anabranch of -def: "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." [] -is_a: RO:0002377 ! distributary of -disjoint_from: RO:0002382 ! proper distributary of -disjoint_from: RO:0002383 ! proper tributary of - -[Typedef] -id: RO:0002379 -name: spatially coextensive with -def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002380 -name: branching part of -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -holds_over_chain: RO:0002377 RO:0002381 -is_a: BFO:0000050 ! part of -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002569 ! has branching part - -[Typedef] -id: RO:0002381 -name: main stem of -def: "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." [] -is_a: BFO:0000050 ! part of -is_a: RO:0002375 ! in branching relationship with - -[Typedef] -id: RO:0002382 -name: proper distributary of -def: "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" [] -is_a: RO:0002377 ! distributary of - -[Typedef] -id: RO:0002383 -name: proper tributary of -def: "x proper_tributary_of y iff x tributary_of y and x does not originate from y" [] -is_a: RO:0002376 ! tributary of - -[Typedef] -id: RO:0002384 -name: has developmental potential involving -def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -is_a: RO:0002324 ! developmentally related to - -[Typedef] -id: RO:0002385 -name: has potential to developmentally contribute to -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: RO:0002386 -name: has potential to developmentally induce -def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: RO:0002387 -name: has potential to develop into -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: RO:0002388 -name: has potential to directly develop into -def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -is_a: RO:0002387 ! has potential to develop into - -[Typedef] -id: RO:0002400 -name: has direct input -def: "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] -holds_over_chain: RO:0002224 RO:0002400 -is_a: RO:0002233 ! has input - -[Typedef] -id: RO:0002401 -name: obsolete has indirect input -is_obsolete: true - -[Typedef] -id: RO:0002402 -name: obsolete has direct output -def: "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " [] -is_obsolete: true - -[Typedef] -id: RO:0002403 -name: obsolete has indirect output -holds_over_chain: RO:0002411 RO:0002402 -is_obsolete: true - -[Typedef] -id: RO:0002404 -name: causally downstream of -def: "inverse of upstream of" [] -is_a: BFO:0000062 ! preceded by -is_a: RO:0002427 ! causally downstream of or within -inverse_of: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002405 -name: immediately causally downstream of -is_a: RO:0002087 ! immediately preceded by -is_a: RO:0002404 ! causally downstream of -inverse_of: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002406 -name: obsolete directly activates -is_obsolete: true -replaced_by: RO:0002629 - -[Typedef] -id: RO:0002407 -name: indirectly positively regulates -def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -holds_over_chain: RO:0002409 RO:0002409 -holds_over_chain: RO:0002629 RO:0002407 -holds_over_chain: RO:0002629 RO:0002629 -is_transitive: true -is_a: RO:0002213 ! positively regulates -is_a: RO:0012012 ! indirectly regulates -transitive_over: RO:0002629 ! directly positively regulates - -[Typedef] -id: RO:0002408 -name: obsolete directly inhibits -is_obsolete: true -replaced_by: RO:0002630 - -[Typedef] -id: RO:0002409 -name: indirectly negatively regulates -def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -holds_over_chain: RO:0002630 RO:0002409 -holds_over_chain: RO:0002630 RO:0002630 -is_transitive: true -is_a: RO:0002212 ! negatively regulates -is_a: RO:0012012 ! indirectly regulates -transitive_over: RO:0002630 ! directly negatively regulates - -[Typedef] -id: RO:0002410 -name: causally related to -def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] - -[Typedef] -id: RO:0002411 -name: causally upstream of -def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] -is_transitive: true -is_a: BFO:0000063 ! precedes -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0002412 -name: immediately causally upstream of -def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] -is_a: RO:0002090 ! immediately precedes -is_a: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0002413 -name: provides input for -def: "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." [] -holds_over_chain: RO:0002402 RO:0002400 -is_a: RO:0002412 ! immediately causally upstream of -is_a: RO:0002414 ! transitively provides input for - -[Typedef] -id: RO:0002414 -name: transitively provides input for -def: "transitive form of directly_provides_input_for" [] -is_transitive: true -is_a: RO:0004047 ! causally upstream of or within, positive effect - -[Typedef] -id: RO:0002418 -name: causally upstream of or within -def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] -synonym: "affects" RELATED [] -is_transitive: true -is_a: RO:0002501 ! causal relation between processes -inverse_of: RO:0002427 ! causally downstream of or within - -[Typedef] -id: RO:0002424 -name: differs in - -[Typedef] -id: RO:0002425 -name: differs in attribute of -is_a: RO:0002424 ! differs in - -[Typedef] -id: RO:0002426 -name: differs in attribute -is_a: RO:0002424 ! differs in - -[Typedef] -id: RO:0002427 -name: causally downstream of or within -def: "inverse of causally upstream of or within" [] -is_transitive: true -is_a: RO:0002501 ! causal relation between processes - -[Typedef] -id: RO:0002428 -name: involved in regulation of -def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -holds_over_chain: RO:0002327 RO:0002211 -holds_over_chain: RO:0002331 RO:0002211 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0002431 ! involved in or involved in regulation of - -[Typedef] -id: RO:0002429 -name: involved in positive regulation of -def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -holds_over_chain: RO:0002327 RO:0002213 -holds_over_chain: RO:0002331 RO:0002213 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002430 -name: involved in negative regulation of -def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -holds_over_chain: RO:0002327 RO:0002212 -holds_over_chain: RO:0002331 RO:0002212 -is_a: RO:0002428 ! involved in regulation of - -[Typedef] -id: RO:0002431 -name: involved in or involved in regulation of -def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -is_a: RO:0002264 ! acts upstream of or within -is_a: RO:0002328 ! functionally related to -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002432 -name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] -synonym: "enables activity in" EXACT [] -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002131 ! overlaps -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002433 -name: contributes to morphology of -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002434 -name: interacts with -def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] -synonym: "in pairwise interaction with" EXACT [] -is_symmetric: true - -[Typedef] -id: RO:0002435 -name: genetically interacts with -is_symmetric: true -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002436 -name: molecularly interacts with -def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -is_symmetric: true -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002437 -name: biotically interacts with -def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] -is_symmetric: true -is_a: RO:0002321 ! ecologically related to -is_a: RO:0002434 ! interacts with - -[Typedef] -id: RO:0002438 -name: trophically interacts with -def: "An interaction relationship in which the partners are related via a feeding relationship." [] -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002439 -name: preys on -def: "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" [] -is_a: RO:0002438 ! trophically interacts with -inverse_of: RO:0002458 ! preyed upon by - -[Typedef] -id: RO:0002440 -name: symbiotically interacts with -def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] -is_symmetric: true -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002441 -name: commensually interacts with -def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0002442 -name: mutualistically interacts with -def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0002443 -name: interacts with via parasite-host interaction -def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0002444 -name: parasite of -synonym: "direct parasite of" EXACT [] -is_a: RO:0002443 ! interacts with via parasite-host interaction -is_a: RO:0002454 ! has host -inverse_of: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0002445 -name: parasitized by -synonym: "directly parasitized by" EXACT [] -is_a: RO:0002443 ! interacts with via parasite-host interaction -is_a: RO:0002453 ! host of - -[Typedef] -id: RO:0002446 -name: participates in a abiotic-biotic interaction with -def: "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." [] -synonym: "semibiotically interacts with" RELATED [] -is_a: RO:0002437 ! biotically interacts with - -[Typedef] -id: RO:0002447 -name: phosphorylates -is_a: RO:0002436 ! molecularly interacts with - -[Typedef] -id: RO:0002448 -name: directly regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] -synonym: "molecularly controls" EXACT [] -is_a: RO:0002436 ! molecularly interacts with -is_a: RO:0011002 ! regulates activity of - -[Typedef] -id: RO:0002449 -name: directly negatively regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] -synonym: "molecularly decreases activity of" EXACT [] -is_a: RO:0002448 ! directly regulates activity of - -[Typedef] -id: RO:0002450 -name: directly positively regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] -synonym: "molecularly increases activity of" EXACT [] -is_a: RO:0002448 ! directly regulates activity of - -[Typedef] -id: RO:0002451 -name: transmitted by -def: "A relationship that holds between a disease and organism" [] -is_a: RO:0002321 ! ecologically related to - -[Typedef] -id: RO:0002452 -name: has symptom -def: "A relation that holds between a disease or an organism and a phenotype" [] -is_a: RO:0002200 ! has phenotype - -[Typedef] -id: RO:0002453 -name: host of -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0002454 -name: has host -def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0002455 -name: pollinates -is_a: RO:0002442 ! mutualistically interacts with -inverse_of: RO:0002456 ! pollinated by - -[Typedef] -id: RO:0002456 -name: pollinated by -is_a: RO:0002442 ! mutualistically interacts with - -[Typedef] -id: RO:0002457 -name: acquires nutrients from -is_a: RO:0002438 ! trophically interacts with -inverse_of: RO:0002469 ! provides nutrients for - -[Typedef] -id: RO:0002458 -name: preyed upon by -def: "inverse of preys on" [] -is_a: RO:0002438 ! trophically interacts with - -[Typedef] -id: RO:0002459 -name: is vector for -is_a: RO:0002574 ! participates in a biotic-biotic interaction with -inverse_of: RO:0002460 ! has vector - -[Typedef] -id: RO:0002460 -name: has vector -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002461 -name: partner in -is_a: RO:0000056 ! participates in - -[Typedef] -id: RO:0002462 -name: subject participant in -is_a: RO:0002461 ! partner in - -[Typedef] -id: RO:0002463 -name: target participant in -is_a: RO:0002461 ! partner in - -[Typedef] -id: RO:0002464 -name: helper property (not for use in curation) - -[Typedef] -id: RO:0002465 -name: is symbiosis -is_a: RO:0002563 ! interaction relation helper property - -[Typedef] -id: RO:0002466 -name: is commensalism -is_a: RO:0002465 ! is symbiosis - -[Typedef] -id: RO:0002467 -name: is mutualism -is_a: RO:0002465 ! is symbiosis - -[Typedef] -id: RO:0002468 -name: is parasitism -is_a: RO:0002465 ! is symbiosis - -[Typedef] -id: RO:0002469 -name: provides nutrients for -is_a: RO:0002438 ! trophically interacts with - -[Typedef] -id: RO:0002470 -name: eats -is_a: RO:0002438 ! trophically interacts with - -[Typedef] -id: RO:0002471 -name: is eaten by -is_a: RO:0002438 ! trophically interacts with - -[Typedef] -id: RO:0002472 -name: is evidence for -def: "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." [] -is_a: RO:0002616 ! related via evidence or inference to -inverse_of: RO:0002558 ! has evidence - -[Typedef] -id: RO:0002473 -name: composed primarily of -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -is_a: BFO:0000051 ! has part - -[Typedef] -id: RO:0002476 -name: child nucleus of -def: "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" [] -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: RO:0002477 -name: child nucleus of in hermaphrodite -def: "A child nucleus relationship in which the cells are part of a hermaphroditic organism" [] -is_a: RO:0002476 ! child nucleus of - -[Typedef] -id: RO:0002478 -name: child nucleus of in male -def: "A child nucleus relationship in which the cells are part of a male organism" [] -is_a: RO:0002476 ! child nucleus of - -[Typedef] -id: RO:0002479 -name: has part that occurs in -def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] -holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} - -[Typedef] -id: RO:0002480 -name: ubiquitinates -def: "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" [] -is_a: RO:0002436 ! molecularly interacts with - -[Typedef] -id: RO:0002481 -name: is kinase activity -is_a: RO:0002564 ! molecular interaction relation helper property - -[Typedef] -id: RO:0002482 -name: is ubiquitination -is_a: RO:0002564 ! molecular interaction relation helper property - -[Typedef] -id: RO:0002485 -name: receives input from -is_a: RO:0002170 ! connected to -inverse_of: RO:0002486 ! sends output to - -[Typedef] -id: RO:0002486 -name: sends output to -is_a: RO:0002170 ! connected to - -[Typedef] -id: RO:0002487 -name: relation between physical entity and a process or stage - -[Typedef] -id: RO:0002488 -name: existence starts during -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -holds_over_chain: RO:0002583 BFO:0000050 -is_a: RO:0002490 ! existence overlaps -is_a: RO:0002496 ! existence starts during or after -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002489 -name: existence starts with -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -is_a: RO:0002488 ! existence starts during - -[Typedef] -id: RO:0002490 -name: existence overlaps -def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] -is_a: RO:0002487 ! relation between physical entity and a process or stage - -[Typedef] -id: RO:0002491 -name: existence starts and ends during -def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -synonym: "exists during" EXACT [] -is_a: RO:0002488 ! existence starts during -is_a: RO:0002492 ! existence ends during - -[Typedef] -id: RO:0002492 -name: existence ends during -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -holds_over_chain: RO:0002593 BFO:0000050 -is_a: RO:0002490 ! existence overlaps -is_a: RO:0002497 ! existence ends during or before -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0002493 -name: existence ends with -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -is_a: RO:0002492 ! existence ends during - -[Typedef] -id: RO:0002494 -name: transformation of -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -is_transitive: true -is_a: RO:0002202 ! develops from - -[Typedef] -id: RO:0002495 -name: immediate transformation of -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -is_a: RO:0002207 ! directly develops from -is_a: RO:0002494 ! transformation of - -[Typedef] -id: RO:0002496 -name: existence starts during or after -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -holds_over_chain: BFO:0000050 RO:0002496 -holds_over_chain: RO:0002258 RO:0002496 -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: BFO:0000050 ! part of -transitive_over: BFO:0000062 ! preceded by -transitive_over: RO:0002082 ! simultaneous with - -[Typedef] -id: RO:0002497 -name: existence ends during or before -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -holds_over_chain: BFO:0000050 RO:0002497 -holds_over_chain: RO:0002286 RO:0002497 -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: BFO:0000050 ! part of -transitive_over: BFO:0000063 ! precedes -transitive_over: RO:0002082 ! simultaneous with - -[Typedef] -id: RO:0002500 -name: causal agent in process -def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -is_a: RO:0002595 ! causal relation between material entity and a process -inverse_of: RO:0002608 ! process has causal agent - -[Typedef] -id: RO:0002501 -name: causal relation between processes -def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002502 -name: depends on - -[Typedef] -id: RO:0002503 -name: towards -def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] -is_a: RO:0002502 ! depends on - -[Typedef] -id: RO:0002505 -name: has intermediate -def: "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" [] -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0002506 -name: causal relation between entities -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002507 -name: determined by -def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] -is_a: BFO:0000050 ! part of -is_a: RO:0002509 ! determined by part of -is_a: RO:0002559 ! causally influenced by -inverse_of: RO:0002508 ! determines - -[Typedef] -id: RO:0002508 -name: determines -def: "inverse of determined by" [] -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002509 -name: determined by part of -def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] -holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} -is_a: RO:0002131 ! overlaps -is_a: RO:0002506 ! causal relation between entities - -[Typedef] -id: RO:0002510 -name: transcribed from -def: "x is transcribed from y if and only if x is synthesized from template y" [] -is_a: RO:0002330 ! genomically related to -inverse_of: RO:0002511 ! transcribed to - -[Typedef] -id: RO:0002511 -name: transcribed to -def: "inverse of transcribed from" [] -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: RO:0002512 -name: ribosomal translation of -def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] -is_a: RO:0002330 ! genomically related to -inverse_of: RO:0002513 ! ribosomally translates to - -[Typedef] -id: RO:0002513 -name: ribosomally translates to -def: "inverse of ribosomal translation of" [] -is_a: RO:0002330 ! genomically related to - -[Typedef] -id: RO:0002514 -name: sequentially related to -def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] - -[Typedef] -id: RO:0002515 -name: sequentially adjacent to -def: "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" [] -is_a: RO:0002527 ! does not overlap sequence of - -[Typedef] -id: RO:0002516 -name: has start sequence -def: "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" [] -is_transitive: true -is_a: RO:0002524 ! has subsequence -inverse_of: RO:0002517 ! is start sequence of - -[Typedef] -id: RO:0002517 -name: is start sequence of -def: "inverse of has start sequence" [] -is_transitive: true -is_a: RO:0002525 ! is subsequence of - -[Typedef] -id: RO:0002518 -name: has end sequence -def: "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" [] -is_transitive: true -is_a: RO:0002524 ! has subsequence -inverse_of: RO:0002519 ! is end sequence of - -[Typedef] -id: RO:0002519 -name: is end sequence of -def: "inverse of has end sequence" [] -is_transitive: true -is_a: RO:0002525 ! is subsequence of - -[Typedef] -id: RO:0002520 -name: is consecutive sequence of -def: "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." [] -is_a: RO:0002524 ! has subsequence - -[Typedef] -id: RO:0002521 -name: is sequentially aligned with -def: "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" [] -is_symmetric: true -is_a: RO:0002514 ! sequentially related to - -[Typedef] -id: RO:0002522 -name: bounds sequence of -def: "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" [] -is_transitive: true -is_a: RO:0002514 ! sequentially related to -inverse_of: RO:0002523 ! is bound by sequence of - -[Typedef] -id: RO:0002523 -name: is bound by sequence of -def: "inverse of bounds sequence of" [] -is_transitive: true -is_a: RO:0002514 ! sequentially related to - -[Typedef] -id: RO:0002524 -name: has subsequence -def: "x has subsequence y iff all of the sequence parts of y are sequence parts of x" [] -is_transitive: true -is_a: BFO:0000051 ! has part -is_a: RO:0002522 ! bounds sequence of -is_a: RO:0002526 ! overlaps sequence of -inverse_of: RO:0002525 ! is subsequence of - -[Typedef] -id: RO:0002525 -name: is subsequence of -def: "inverse of has subsequence" [] -is_transitive: true -is_a: BFO:0000050 ! part of -is_a: RO:0002523 ! is bound by sequence of -is_a: RO:0002526 ! overlaps sequence of - -[Typedef] -id: RO:0002526 -name: overlaps sequence of -def: "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." [] -holds_over_chain: RO:0002524 RO:0002525 -is_symmetric: true -is_a: RO:0002131 ! overlaps -is_a: RO:0002514 ! sequentially related to - -[Typedef] -id: RO:0002527 -name: does not overlap sequence of -def: "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." [] -is_symmetric: true -is_a: RO:0002514 ! sequentially related to - -[Typedef] -id: RO:0002528 -name: is upstream of sequence of -def: "inverse of downstream of sequence of" [] -is_transitive: true -is_a: RO:0002527 ! does not overlap sequence of - -[Typedef] -id: RO:0002529 -name: is downstream of sequence of -def: "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." [] -is_transitive: true -is_a: RO:0002527 ! does not overlap sequence of -inverse_of: RO:0002529 ! is downstream of sequence of - -[Typedef] -id: RO:0002530 -name: is immediately downstream of sequence of -def: "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" [] -is_a: RO:0002515 ! sequentially adjacent to -is_a: RO:0002529 ! is downstream of sequence of - -[Typedef] -id: RO:0002531 -name: is immediately upstream of sequence of -def: "inverse of immediately downstream of" [] -is_a: RO:0002515 ! sequentially adjacent to -is_a: RO:0002528 ! is upstream of sequence of - -[Typedef] -id: RO:0002551 -name: has skeleton -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -is_a: BFO:0000051 ! has part -inverse_of: RO:0002576 ! skeleton of -is_asymmetric: true - -[Typedef] -id: RO:0002552 -name: results in ending of -def: "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." [] -is_a: RO:0002295 ! results in developmental progression of -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002553 -name: hyperparasite of -def: "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" [] -synonym: "epiparasite of" RELATED [] -synonym: "hyperparasitoid of" NARROW [] -holds_over_chain: RO:0002444 RO:0002444 -is_a: RO:0002454 ! has host -inverse_of: RO:0002554 ! hyperparasitized by - -[Typedef] -id: RO:0002554 -name: hyperparasitized by -def: "inverse of hyperparasite of" [] -synonym: "has epiparasite" RELATED [] -synonym: "has hyperparasite" RELATED [] -synonym: "hyperparasitoidized by" RELATED [] -holds_over_chain: RO:0002445 RO:0002445 -is_a: RO:0002453 ! host of - -[Typedef] -id: RO:0002555 -name: allelopath of -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002556 -name: pathogen of -is_a: RO:0002454 ! has host -inverse_of: RO:0002557 ! has pathogen - -[Typedef] -id: RO:0002557 -name: has pathogen -is_a: RO:0002453 ! host of - -[Typedef] -id: RO:0002558 -name: has evidence -def: "inverse of is evidence for" [] -is_a: RO:0002616 ! related via evidence or inference to - -[Typedef] -id: RO:0002559 -name: causally influenced by -is_a: RO:0002506 ! causal relation between entities -inverse_of: RO:0002566 ! causally influences - -[Typedef] -id: RO:0002563 -name: interaction relation helper property -is_a: RO:0002464 ! helper property (not for use in curation) - -[Typedef] -id: RO:0002564 -name: molecular interaction relation helper property -is_a: RO:0002563 ! interaction relation helper property - -[Typedef] -id: RO:0002565 -name: results in movement of -def: "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" [] -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002566 -name: causally influences -def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -is_a: RO:0002506 ! causal relation between entities - -[Typedef] -id: RO:0002567 -name: biomechanically related to -def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0002568 -name: has muscle antagonist -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: RO:0002569 -name: has branching part -def: "inverse of branching part of" [] -is_transitive: true -is_a: BFO:0000051 ! has part -is_a: RO:0002375 ! in branching relationship with - -[Typedef] -id: RO:0002570 -name: conduit for -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -is_a: RO:0002131 ! overlaps - -[Typedef] -id: RO:0002571 -name: lumen of -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -is_a: BFO:0000050 ! part of - -[Typedef] -id: RO:0002572 -name: luminal space of -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -is_a: RO:0002571 ! lumen of - -[Typedef] -id: RO:0002573 -name: has modifier -def: "A relation that holds between an attribute or a qualifier and another attribute." [] - -[Typedef] -id: RO:0002574 -name: participates in a biotic-biotic interaction with -is_a: RO:0002437 ! biotically interacts with - -[Typedef] -id: RO:0002576 -name: skeleton of -def: "inverse of has skeleton" [] -is_a: BFO:0000050 ! part of - -[Typedef] -id: RO:0002578 -name: directly regulates -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -is_a: RO:0002211 ! regulates -is_a: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002583 -name: existence starts at end of -def: "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." [] -is_a: RO:0002496 ! existence starts during or after - -[Typedef] -id: RO:0002584 -name: has part structure that is capable of -def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -holds_over_chain: BFO:0000051 RO:0002215 -is_a: RO:0002328 ! functionally related to -is_a: RO:0002595 ! causal relation between material entity and a process - -[Typedef] -id: RO:0002585 -name: results in closure of -is_a: RO:0002295 ! results in developmental progression of -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002586 -name: results in breakdown of -def: "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" [] -is_a: RO:0002233 ! has input - -[Typedef] -id: RO:0002587 -name: results in synthesis of -is_a: RO:0002297 ! results in formation of - -[Typedef] -id: RO:0002588 -name: results in assembly of -is_a: RO:0002297 ! results in formation of -is_a: RO:0002592 ! results in organization of - -[Typedef] -id: RO:0002589 -name: results in catabolism of -def: "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." [] -is_a: RO:0002586 ! results in breakdown of - -[Typedef] -id: RO:0002590 -name: results in disassembly of -is_a: RO:0002586 ! results in breakdown of -is_a: RO:0002592 ! results in organization of - -[Typedef] -id: RO:0002591 -name: results in remodeling of -is_a: RO:0002233 ! has input -is_a: RO:0002592 ! results in organization of - -[Typedef] -id: RO:0002592 -name: results in organization of -def: "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" [] -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0002593 -name: existence ends at start of -def: "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." [] -is_a: RO:0002497 ! existence ends during or before - -[Typedef] -id: RO:0002595 -name: causal relation between material entity and a process -def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002596 -name: capable of regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -holds_over_chain: RO:0002215 RO:0002211 -is_a: RO:0002500 ! causal agent in process - -[Typedef] -id: RO:0002597 -name: capable of negatively regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -holds_over_chain: RO:0002215 RO:0002212 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002598 -name: capable of positively regulating -def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -holds_over_chain: RO:0002215 RO:0002213 -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0002599 -name: capable of inhibiting or preventing pathological process -def: "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." [] -is_a: RO:0002597 ! capable of negatively regulating - -[Typedef] -id: RO:0002600 -name: capable of upregulating or causing pathological process -def: "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." [] -is_a: RO:0002598 ! capable of positively regulating - -[Typedef] -id: RO:0002606 -name: is substance that treats -def: "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." [] -is_a: RO:0002599 ! capable of inhibiting or preventing pathological process - -[Typedef] -id: RO:0002607 -name: is marker for -def: "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." [] -is_a: RO:0002610 ! correlated with - -[Typedef] -id: RO:0002608 -name: process has causal agent -def: "Inverse of 'causal agent in process'" [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0002609 -name: obsolete related via dependence to -def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] -is_obsolete: true - -[Typedef] -id: RO:0002610 -name: correlated with -def: "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] - -[Typedef] -id: RO:0002614 -name: is evidence with support from -def: "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." [] -is_a: RO:0002616 ! related via evidence or inference to - -[Typedef] -id: RO:0002615 -name: has model -def: "Inverse of is-model-of" [] -inverse_of: RO:0003301 ! has role in modeling - -[Typedef] -id: RO:0002616 -name: related via evidence or inference to - -[Typedef] -id: RO:0002618 -name: visits -is_a: RO:0002574 ! participates in a biotic-biotic interaction with -inverse_of: RO:0002619 ! visited by - -[Typedef] -id: RO:0002619 -name: visited by -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002622 -name: visits flowers of -is_a: RO:0002618 ! visits -inverse_of: RO:0002623 ! has flowers visited by - -[Typedef] -id: RO:0002623 -name: has flowers visited by -is_a: RO:0002619 ! visited by - -[Typedef] -id: RO:0002624 -name: lays eggs in -is_a: RO:0002444 ! parasite of -is_a: RO:0002618 ! visits -inverse_of: RO:0002625 ! has eggs laid in by - -[Typedef] -id: RO:0002625 -name: has eggs laid in by -is_a: RO:0002445 ! parasitized by -is_a: RO:0002619 ! visited by - -[Typedef] -id: RO:0002626 -name: kills -is_a: RO:0002574 ! participates in a biotic-biotic interaction with -inverse_of: RO:0002627 ! is killed by - -[Typedef] -id: RO:0002627 -name: is killed by -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002629 -name: directly positively regulates -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -is_a: RO:0002213 ! positively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002630 -name: directly negatively regulates -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -is_a: RO:0002212 ! negatively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002632 -name: ectoparasite of -def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] -is_a: RO:0002444 ! parasite of -inverse_of: RO:0002633 ! has ectoparasite - -[Typedef] -id: RO:0002633 -name: has ectoparasite -def: "inverse of ectoparasite of" [] -is_a: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0002634 -name: endoparasite of -synonym: "lives inside of" RELATED [] -is_a: RO:0002444 ! parasite of -inverse_of: RO:0002635 ! has endoparasite - -[Typedef] -id: RO:0002635 -name: has endoparasite -is_a: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0002636 -name: mesoparasite of -def: "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" [] -is_a: RO:0002444 ! parasite of -inverse_of: RO:0002637 ! has mesoparasite - -[Typedef] -id: RO:0002637 -name: has mesoparasite -def: "inverse of mesoparasite of" [] -is_a: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0002638 -name: intercellular endoparasite of -def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] -is_a: RO:0002634 ! endoparasite of -inverse_of: RO:0002639 ! has intercellular endoparasite - -[Typedef] -id: RO:0002639 -name: has intercellular endoparasite -def: "inverse of intercellular endoparasite of" [] -is_a: RO:0002635 ! has endoparasite - -[Typedef] -id: RO:0002640 -name: intracellular endoparasite of -def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] -is_a: RO:0002634 ! endoparasite of -inverse_of: RO:0002641 ! has intracellular endoparasite - -[Typedef] -id: RO:0002641 -name: has intracellular endoparasite -def: "inverse of intracellular endoparasite of" [] -is_a: RO:0002635 ! has endoparasite - -[Typedef] -id: RO:0002801 -name: co-roosts with -def: "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." [] -is_symmetric: true -is_a: RO:0008506 ! ecologically co-occurs with - -[Typedef] -id: RO:0003000 -name: produces -def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] -inverse_of: RO:0003001 ! produced by - -[Typedef] -id: RO:0003001 -name: produced by -def: "a produced_by b iff some process that occurs_in b has_output a." [] - -[Typedef] -id: RO:0003002 -name: represses expression of -def: "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." [] -is_a: RO:0002449 ! directly negatively regulates activity of - -[Typedef] -id: RO:0003003 -name: increases expression of -def: "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." [] -is_a: RO:0002450 ! directly positively regulates activity of - -[Typedef] -id: RO:0003301 -name: has role in modeling -def: "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." [] -is_asymmetric: true - -[Typedef] -id: RO:0003302 -name: causes or contributes to condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0003303 -name: causes condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." [] -is_a: RO:0003302 ! causes or contributes to condition - -[Typedef] -id: RO:0003304 -name: contributes to condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." [] -is_a: RO:0003302 ! causes or contributes to condition - -[Typedef] -id: RO:0003305 -name: contributes to severity of condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." [] -is_a: RO:0003304 ! contributes to condition - -[Typedef] -id: RO:0003306 -name: contributes to frequency of condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." [] -is_a: RO:0003304 ! contributes to condition - -[Typedef] -id: RO:0003307 -name: ameliorates condition -def: "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." [] -is_a: RO:0003305 ! contributes to severity of condition - -[Typedef] -id: RO:0003308 -name: correlated with condition -def: "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." [] -is_a: RO:0002610 ! correlated with - -[Typedef] -id: RO:0003309 -name: exacerbates condition -def: "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." [] -is_a: RO:0003305 ! contributes to severity of condition - -[Typedef] -id: RO:0003310 -name: condition ameliorated by -def: "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0003311 -name: condition exacerbated by -def: "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." [] -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0004000 -name: condition has genetic basis in -is_a: RO:0002410 ! causally related to -inverse_of: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004001 -name: has material basis in gain of function germline mutation in -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004011 ! is causal gain of function germline mutation of in - -[Typedef] -id: RO:0004002 -name: has material basis in loss of function germline mutation in -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004012 ! is causal loss of function germline mutation of in - -[Typedef] -id: RO:0004003 -name: has material basis in germline mutation in -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004013 ! is causal germline mutation in - -[Typedef] -id: RO:0004004 -name: has material basis in somatic mutation in -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004014 ! is causal somatic mutation in - -[Typedef] -id: RO:0004005 -name: has major susceptibility factor -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004015 ! is causal susceptibility factor for - -[Typedef] -id: RO:0004006 -name: has partial material basis in germline mutation in -is_a: RO:0004000 ! condition has genetic basis in -inverse_of: RO:0004016 ! is causal germline mutation partially giving rise to - -[Typedef] -id: RO:0004007 -name: has primary input or output -def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0004008 -name: has primary output -def: "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} -is_a: RO:0002234 ! has output -is_a: RO:0004007 ! has primary input or output - -[Typedef] -id: RO:0004009 -name: has primary input -def: "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c." [GOC:cjm, GOC:dph, GOC:kva, GOC:pt] {comment="PMID:27812932"} -is_a: RO:0002233 ! has input -is_a: RO:0004007 ! has primary input or output - -[Typedef] -id: RO:0004010 -name: is genetic basis for condition -is_a: RO:0004018 ! is basis for realizable - -[Typedef] -id: RO:0004011 -name: is causal gain of function germline mutation of in -def: "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004012 -name: is causal loss of function germline mutation of in -def: "Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004013 -name: is causal germline mutation in -def: "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." [] -is_a: RO:0003303 ! causes condition -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004014 -name: is causal somatic mutation in -def: "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." [] -is_a: RO:0003303 ! causes condition -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004015 -name: is causal susceptibility factor for -def: "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." [] -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004016 -name: is causal germline mutation partially giving rise to -def: "Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]." [] -is_a: RO:0003304 ! contributes to condition -is_a: RO:0004010 ! is genetic basis for condition - -[Typedef] -id: RO:0004017 -name: realizable has basis in -is_a: RO:0002410 ! causally related to -inverse_of: RO:0004018 ! is basis for realizable - -[Typedef] -id: RO:0004018 -name: is basis for realizable -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0004019 -name: disease has basis in -is_a: RO:0004017 ! realizable has basis in -is_a: RO:0004023 ! causal relationship with disease as subject - -[Typedef] -id: RO:0004020 -name: disease has basis in dysfunction of -def: "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." [] -is_a: RO:0004019 ! disease has basis in - -[Typedef] -id: RO:0004021 -name: disease has basis in disruption of -def: "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." [] -is_a: RO:0004019 ! disease has basis in - -[Typedef] -id: RO:0004022 -name: disease has basis in feature -def: "A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature." [] -is_a: RO:0002200 ! has phenotype -is_a: RO:0004019 ! disease has basis in - -[Typedef] -id: RO:0004023 -name: causal relationship with disease as subject -is_a: RO:0002410 ! causally related to -is_a: RO:0040035 ! disease relationship - -[Typedef] -id: RO:0004024 -name: disease causes disruption of -def: "A relationship between a disease and a process where the disease process disrupts the execution of the process." [] -holds_over_chain: RO:0004025 RO:0002215 -is_a: RO:0004023 ! causal relationship with disease as subject -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0004025 -name: disease causes dysfunction of -is_a: RO:0004023 ! causal relationship with disease as subject -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0004026 -name: disease has location -def: "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." [] -is_a: RO:0040035 ! disease relationship - -[Typedef] -id: RO:0004027 -name: disease has inflammation site -def: "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" [] -is_a: RO:0004026 ! disease has location - -[Typedef] -id: RO:0004028 -name: realized in response to stimulus -def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] -holds_over_chain: RO:0009501 RO:0002233 -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0004029 -name: disease has feature -def: "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." [] -is_a: RO:0040035 ! disease relationship - -[Typedef] -id: RO:0004030 -name: disease arises from alteration in structure -def: "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." [] -is_a: RO:0004019 ! disease has basis in - -[Typedef] -id: RO:0004031 -name: enables subfunction -def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] -holds_over_chain: RO:0002327 BFO:0000051 -is_a: RO:0002328 ! functionally related to - -[Typedef] -id: RO:0004032 -name: acts upstream of or within, positive effect -holds_over_chain: RO:0002327 RO:0004047 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0004033 -name: acts upstream of or within, negative effect -holds_over_chain: RO:0002327 RO:0004046 -is_a: RO:0002264 ! acts upstream of or within - -[Typedef] -id: RO:0004034 -name: acts upstream of, positive effect -def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] -holds_over_chain: RO:0002327 RO:0002304 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004032 ! acts upstream of or within, positive effect - -[Typedef] -id: RO:0004035 -name: acts upstream of, negative effect -def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] -holds_over_chain: RO:0002327 RO:0002305 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004033 ! acts upstream of or within, negative effect - -[Typedef] -id: RO:0004046 -name: causally upstream of or within, negative effect -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0004047 -name: causally upstream of or within, positive effect -is_a: RO:0002418 ! causally upstream of or within - -[Typedef] -id: RO:0004096 -name: DEPRECATED inheres in -is_obsolete: true - -[Typedef] -id: RO:0004097 -name: DEPRECATED bearer of -is_obsolete: true - -[Typedef] -id: RO:0007000 -name: has driver -def: "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." [] - -[Typedef] -id: RO:0007001 -name: has disease driver -def: "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." [] -is_a: RO:0007000 ! has driver - -[Typedef] -id: RO:0008501 -name: epiphyte of -def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] -is_a: RO:0002440 ! symbiotically interacts with -inverse_of: RO:0008502 ! has epiphyte - -[Typedef] -id: RO:0008502 -name: has epiphyte -def: "inverse of epiphyte of" [] -is_a: RO:0002440 ! symbiotically interacts with - -[Typedef] -id: RO:0008503 -name: kleptoparasite of -def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] -is_a: RO:0002444 ! parasite of -inverse_of: RO:0008504 ! kleptoparasitized by - -[Typedef] -id: RO:0008504 -name: kleptoparasitized by -def: "inverse of kleptoparasite of" [] -is_a: RO:0002445 ! parasitized by - -[Typedef] -id: RO:0008505 -name: creates habitat for -def: "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." [] -is_a: RO:0002321 ! ecologically related to - -[Typedef] -id: RO:0008506 -name: ecologically co-occurs with -def: "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." [] -is_symmetric: true -is_a: RO:0002321 ! ecologically related to - -[Typedef] -id: RO:0008507 -name: lays eggs on -def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] -is_a: RO:0002618 ! visits -inverse_of: RO:0008508 ! has eggs laid on by - -[Typedef] -id: RO:0008508 -name: has eggs laid on by -def: "inverse of lays eggs on" [] -is_a: RO:0002619 ! visited by - -[Typedef] -id: RO:0009001 -name: has substance added -def: "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." [] - -[Typedef] -id: RO:0009002 -name: has substance removed -def: "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." [] - -[Typedef] -id: RO:0009003 -name: immersed in -def: "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." [] - -[Typedef] -id: RO:0009004 -name: has consumer -def: "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." [] - -[Typedef] -id: RO:0009005 -name: has primary substance added -def: "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." [] -is_a: RO:0009001 ! has substance added - -[Typedef] -id: RO:0009501 -name: realized in response to -def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] -holds_over_chain: BFO:0000054 RO:0002404 -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0010001 -name: generically depends on -def: "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." [] -synonym: "g-depends on" EXACT [] -holds_over_chain: RO:0000052 RO:0000058 -inverse_of: RO:0010002 ! is carrier of - -[Typedef] -id: RO:0010002 -name: is carrier of -def: "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" [] -holds_over_chain: RO:0000059 RO:0000053 - -[Typedef] -id: RO:0011002 -name: regulates activity of -def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0011003 -name: regulates quantity of -def: "The entity A has an activity that regulates the quantity or abundance or concentration of the entity B." [] -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0011004 -name: indirectly regulates activity of -def: "The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B." [] -is_a: RO:0011002 ! regulates activity of - -[Typedef] -id: RO:0011007 -name: decreases by repression quantity of -def: "The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B." [] -is_a: RO:0011023 ! indirectly negatively regulates quantity of - -[Typedef] -id: RO:0011008 -name: increases by expression quantity of -def: "The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B." [] -is_a: RO:0011024 ! indirectly positively regulates quantity of - -[Typedef] -id: RO:0011009 -name: directly positively regulates quantity of -def: "The entity A has an activity that directly positively regulates the quantity of B." [] -is_a: RO:0011021 ! directly regulates quantity of - -[Typedef] -id: RO:0011010 -name: directly negatively regulates quantity of -def: "The entity A has an activity that directly negatively regulates the quantity of B." [] -is_a: RO:0011021 ! directly regulates quantity of - -[Typedef] -id: RO:0011013 -name: indirectly positively regulates activity of -def: "The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B." [] -is_a: RO:0011004 ! indirectly regulates activity of - -[Typedef] -id: RO:0011014 -name: destabilizes quantity of -def: "An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it." [] -is_a: RO:0011010 ! directly negatively regulates quantity of - -[Typedef] -id: RO:0011015 -name: stabilizes quantity of -def: "An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it." [] -is_a: RO:0011009 ! directly positively regulates quantity of - -[Typedef] -id: RO:0011016 -name: indirectly negatively regulates activity of -def: "The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B." [] -is_a: RO:0011004 ! indirectly regulates activity of - -[Typedef] -id: RO:0011021 -name: directly regulates quantity of -def: "The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B." [] -is_a: RO:0011003 ! regulates quantity of - -[Typedef] -id: RO:0011022 -name: indirectly regulates quantity of -def: "The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B." [] -is_a: RO:0011003 ! regulates quantity of - -[Typedef] -id: RO:0011023 -name: indirectly negatively regulates quantity of -def: "The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B." [] -is_a: RO:0011022 ! indirectly regulates quantity of - -[Typedef] -id: RO:0011024 -name: indirectly positively regulates quantity of -def: "The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B." [] -is_a: RO:0011022 ! indirectly regulates quantity of - -[Typedef] -id: RO:0012000 -name: has small molecule regulator -def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] -is_a: RO:0000057 ! has participant -inverse_of: RO:0012004 ! is small molecule regulator of - -[Typedef] -id: RO:0012001 -name: has small molecule activator -def: "a relation between a process and a continuant, in which the process is activated by the small molecule continuant" [] -is_a: RO:0012000 ! has small molecule regulator -inverse_of: RO:0012005 ! is small molecule activator of - -[Typedef] -id: RO:0012002 -name: has small molecule inhibitor -def: "a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant" [] -is_a: RO:0012000 ! has small molecule regulator -inverse_of: RO:0012006 ! is small molecule inhibitor of - -[Typedef] -id: RO:0012003 -name: acts on population of -def: "p acts on population of c iff c' is a collection, has members of type c, and p has participant c" [] -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:0012004 -name: is small molecule regulator of -def: "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" [] -is_a: RO:0002596 ! capable of regulating - -[Typedef] -id: RO:0012005 -name: is small molecule activator of -def: "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" [] -is_a: RO:0002598 ! capable of positively regulating -is_a: RO:0012004 ! is small molecule regulator of - -[Typedef] -id: RO:0012006 -name: is small molecule inhibitor of -def: "a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process" [] -is_a: RO:0002597 ! capable of negatively regulating -is_a: RO:0012004 ! is small molecule regulator of - -[Typedef] -id: RO:0012007 -name: results in adhesion of -def: "The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities." [] -is_a: RO:0040036 ! results in changes to anatomical or cellular structure - -[Typedef] -id: RO:0012008 -name: results in fusion of -is_a: RO:0002592 ! results in organization of - -[Typedef] -id: RO:0012009 -name: constitutively upstream of -def: "p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant." [] -is_a: RO:0002304 ! causally upstream of, positive effect - -[Typedef] -id: RO:0012010 -name: removes input for -def: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q." [] -is_a: RO:0002305 ! causally upstream of, negative effect - -[Typedef] -id: RO:0012011 -name: indirectly causally upstream of -def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] -is_a: RO:0002411 ! causally upstream of - -[Typedef] -id: RO:0012012 -name: indirectly regulates -def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] -is_a: RO:0002211 ! regulates -is_a: RO:0012011 ! indirectly causally upstream of - -[Typedef] -id: RO:0013001 -name: has synaptic IO in region -def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] -synonym: "has synaptic input or output in" EXACT [] -is_a: RO:0002130 ! has synaptic terminal in -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0013002 -name: receives synaptic input in region -def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region." [] -is_a: RO:0002110 ! has postsynaptic terminal in -is_a: RO:0013001 ! has synaptic IO in region -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0013003 -name: sends synaptic output to region -def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region." [] -is_a: RO:0002113 ! has presynaptic terminal in -is_a: RO:0013001 ! has synaptic IO in region -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0013004 -name: has synaptic IO throughout -def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion)." [] -is_a: RO:0013001 ! has synaptic IO in region - -[Typedef] -id: RO:0013005 -name: receives synaptic input throughout -def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." [] -is_a: RO:0013002 ! receives synaptic input in region -is_a: RO:0013004 ! has synaptic IO throughout - -[Typedef] -id: RO:0013006 -name: sends synaptic output throughout -def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." [] -is_a: RO:0013003 ! sends synaptic output to region -is_a: RO:0013004 ! has synaptic IO throughout - -[Typedef] -id: RO:0013007 -name: has sensory dendrite in -def: "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." [] -synonym: "has sensory dendrite location" EXACT [] -synonym: "has sensory terminal in" EXACT [] -synonym: "has sensory terminal location" EXACT [] -is_a: RO:0002360 ! has dendrite location -transitive_over: BFO:0000050 ! part of - -[Typedef] -id: RO:0013008 -name: receives synaptic input from neuron -def: "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." [] -is_a: RO:0002103 ! synapsed by -inverse_of: RO:0013009 ! sends synaptic output to cell - -[Typedef] -id: RO:0013009 -name: sends synaptic output to cell -def: "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." [] -is_a: RO:0002120 ! synapsed to - -[Typedef] -id: RO:0014001 -name: disease has infectious agent -def: "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." [] -is_a: RO:0004019 ! disease has basis in - -[Typedef] -id: RO:0015001 -name: has exemplar data -def: "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." [] -inverse_of: RO:0015002 ! exemplar data of -transitive_over: RO:0015003 ! subcluster of - -[Typedef] -id: RO:0015002 -name: exemplar data of - -[Typedef] -id: RO:0015003 -name: subcluster of -def: "A relation between a group and another group it is part of but does not fully constitute." [] -is_transitive: true -is_a: BFO:0000050 ! part of - -[Typedef] -id: RO:0015004 -name: has characterizing marker set -def: "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." [] -synonym: "has marker gene combination" EXACT [] -synonym: "has marker signature set" EXACT [] - -[Typedef] -id: RO:0015006 -name: different in magnitude relative to -def: "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] - -[Typedef] -id: RO:0015007 -name: increased in magnitude relative to -def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] -is_a: RO:0015006 ! different in magnitude relative to - -[Typedef] -id: RO:0015008 -name: decreased in magnitude relative to -def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] -is_a: RO:0015006 ! different in magnitude relative to - -[Typedef] -id: RO:0015009 -name: similar in magnitude relative to -def: "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [https://orcid.org/0000-0002-6601-2165] - -[Typedef] -id: RO:0015010 -name: has relative magnitude - -[Typedef] -id: RO:0015011 -name: has cross section -def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [https://orcid.org/0000-0002-6601-2165] - -[Typedef] -id: RO:0015012 -name: reciprocal of -def: "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e." [https://orcid.org/0000-0002-6601-2165] - -[Typedef] -id: RO:0015015 -name: has high plasma membrane amount -def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -is_a: RO:0002104 ! has plasma membrane part - -[Typedef] -id: RO:0015016 -name: has low plasma membrane amount -def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -is_a: RO:0002104 ! has plasma membrane part - -[Typedef] -id: RO:0016001 -name: has phenotype or disease - -[Typedef] -id: RO:0016002 -name: has disease -def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] -is_a: RO:0016001 ! has phenotype or disease - -[Typedef] -id: RO:0016004 -name: has exposure medium -def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] -is_a: RO:0002244 ! related via exposure to - -[Typedef] -id: RO:0017001 -name: device utilizes material -def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] -synonym: "utilizes" BROAD [] -holds_over_chain: RO:0002215 RO:0002233 - -[Typedef] -id: RO:0018001 -name: is myristoyltransferase activity -def: "Helper relation for OWL definition of RO:0018002 myristoylates" [] -is_a: RO:0002564 ! molecular interaction relation helper property - -[Typedef] -id: RO:0018002 -name: myristoylates -def: "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" [] -is_a: RO:0002436 ! molecularly interacts with -inverse_of: RO:0018003 ! myristoylated by - -[Typedef] -id: RO:0018003 -name: myristoylated by -def: "inverse of myristoylates" [] - -[Typedef] -id: RO:0018027 -name: is agonist of -def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" [] -is_a: RO:0002450 ! directly positively regulates activity of - -[Typedef] -id: RO:0018028 -name: is inverse agonist of -def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" [] -is_a: RO:0002449 ! directly negatively regulates activity of - -[Typedef] -id: RO:0018029 -name: is antagonist of -def: "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level" [] -is_a: RO:0002449 ! directly negatively regulates activity of - -[Typedef] -id: RO:0019000 -name: regulates characteristic -def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] -holds_over_chain: RO:0002211 RO:0019000 -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0019001 -name: positively regulates characteristic -def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] -holds_over_chain: RO:0002213 RO:0019001 -is_a: RO:0019000 ! regulates characteristic - -[Typedef] -id: RO:0019002 -name: negatively regulates characteristic -def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] -holds_over_chain: RO:0002212 RO:0019001 -holds_over_chain: RO:0002213 RO:0019002 -is_a: RO:0019000 ! regulates characteristic - -[Typedef] -id: RO:0019501 -name: confers susceptibility to condition -def: "Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition." [] -is_a: RO:0003304 ! contributes to condition - -[Typedef] -id: RO:0040035 -name: disease relationship -def: "This relation groups relations between diseases and any other kind of entity." [] - -[Typedef] -id: RO:0040036 -name: results in changes to anatomical or cellular structure -def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] -is_a: RO:0000057 ! has participant - -[Typedef] -id: RO:HOM0000000 -name: in similarity relationship with -def: "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000000] -synonym: "correspondence" RELATED [http://dx.doi.org/10.1007/BF02814479] -synonym: "resemblance" RELATED [] -synonym: "sameness" EXACT [] -synonym: "similar to" EXACT [] -is_symmetric: true - -[Typedef] -id: RO:HOM0000001 -name: in homology relationship with -def: "Similarity that results from common evolutionary origin." [http://dx.doi.org/10.1002/bies.950180611, http://dx.doi.org/10.1002/jmor.1051730307, http://dx.doi.org/10.1007/BF02814480, http://purl.obolibrary.org/obo/HOM_0000001] -synonym: "homologous to" EXACT [] -is_symmetric: true -is_a: RO:0002158 ! shares ancestor with -is_a: RO:HOM0000000 ! in similarity relationship with -disjoint_from: RO:HOM0000002 ! in homoplasy relationship with - -[Typedef] -id: RO:HOM0000002 -name: in homoplasy relationship with -def: "Similarity that results from independent evolution." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000002] -synonym: "analogy" RELATED [] -synonym: "homoplasous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000000 ! in similarity relationship with - -[Typedef] -id: RO:HOM0000003 -name: in homocracy relationship with -def: "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/s00427-003-0301-4, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000003] -synonym: "homocracous to" EXACT [] -is_symmetric: true -is_a: RO:0002320 ! evolutionarily related to -is_a: RO:HOM0000000 ! in similarity relationship with - -[Typedef] -id: RO:HOM0000004 -name: in convergence relationship with -def: "Homoplasy that involves different underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000004] -synonym: "analogy" RELATED [] -is_symmetric: true -is_a: RO:HOM0000002 ! in homoplasy relationship with - -[Typedef] -id: RO:HOM0000005 -name: in parallelism relationship with -def: "Homoplasy that involves homologous underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000005] -synonym: "parallel evolution" EXACT [] -is_symmetric: true -is_a: RO:HOM0000002 ! in homoplasy relationship with - -[Typedef] -id: RO:HOM0000006 -name: in structural homology relationship with -def: "Homology that is defined by similarity with regard to selected structural parameters." [http://dx.doi.org/10.1016/j.jhevol.2006.11.014, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000006, ISBN:0123195837] -synonym: "idealistic homology" RELATED [] -synonym: "structural homologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000001 ! in homology relationship with - -[Typedef] -id: RO:HOM0000007 -name: in historical homology relationship with -def: "Homology that is defined by common descent." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://purl.obolibrary.org/obo/HOM_0000007, ISBN:0123195837] -synonym: "cladistic homology" EXACT [] -synonym: "historical homologous to" EXACT [] -synonym: "homology" BROAD [] -synonym: "phylogenetic homology" EXACT [] -synonym: "taxic homology" EXACT [] -synonym: "true homology" RELATED [] -is_symmetric: true -is_a: RO:HOM0000001 ! in homology relationship with - -[Typedef] -id: RO:HOM0000008 -name: in biological homology relationship with -def: "Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000008] -synonym: "biological homologous to" EXACT [] -synonym: "transformational homology" RELATED [] -is_symmetric: true -is_a: RO:HOM0000001 ! in homology relationship with - -[Typedef] -id: RO:HOM0000009 -name: in reversal relationship with -def: "Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000009] -synonym: "atavism" EXACT [] -synonym: "reversion" RELATED [] -synonym: "rudiment" EXACT [] -is_symmetric: true -is_a: RO:HOM0000002 ! in homoplasy relationship with - -[Typedef] -id: RO:HOM0000010 -name: in syntenic homology relationship with -def: "Structural homology that is detected by similarity in content and organization between chromosomes." [http://purl.obolibrary.org/obo/HOM_0000010, MeSH:Synteny] -synonym: "syntenic homologous to" EXACT [] -synonym: "synteny" RELATED [] -is_symmetric: true -is_a: RO:HOM0000006 ! in structural homology relationship with - -[Typedef] -id: RO:HOM0000011 -name: in paralogy relationship with -def: "Historical homology that involves genes that diverged after a duplication event." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000011, http://www.ncbi.nlm.nih.gov/pubmed/5449325] -synonym: "paralogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with -disjoint_from: RO:HOM0000017 ! in orthology relationship with - -[Typedef] -id: RO:HOM0000012 -name: in syntenic paralogy relationship with -def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20001215)288\:4<345\:\:AID-JEZ7>3.0.CO;2-Y, http://dx.doi.org/10.1186/1471-213X-7-100, http://purl.obolibrary.org/obo/HOM_0000012] -synonym: "duplicon" RELATED [] -synonym: "paralogon" RELATED [] -synonym: "syntenic paralogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000010 ! in syntenic homology relationship with -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000013 -name: in syntenic orthology relationship with -def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] -synonym: "syntenic orthologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000010 ! in syntenic homology relationship with - -[Typedef] -id: RO:HOM0000014 -name: in partial homology relationship with -def: "Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous." [http://purl.obolibrary.org/obo/HOM_0000014, ISBN:0123195837, ISBN:978-0471984931] -synonym: "fractional homology" EXACT [] -synonym: "mixed homology" RELATED [] -synonym: "modular homology" RELATED [] -synonym: "partial correspondence" RELATED [] -synonym: "partial homologous to" EXACT [] -synonym: "percent homology" RELATED [] -synonym: "segmental homology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000006 ! in structural homology relationship with - -[Typedef] -id: RO:HOM0000015 -name: in protein structural homology relationship with -def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [http://dx.doi.org/10.1016/0022-2836(76)90195-9, http://purl.obolibrary.org/obo/HOM_0000015] -synonym: "protein structural homologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000006 ! in structural homology relationship with - -[Typedef] -id: RO:HOM0000016 -name: in non functional homology relationship with -def: "Structural homology that involves a pseudogenic feature and its functional ancestor." [http://purl.obolibrary.org/obo/HOM_0000016, SO:non_functional_homolog_of] -synonym: "non functional homologous to" EXACT [] -synonym: "pseudogene" BROAD [] -is_symmetric: true -is_a: RO:HOM0000006 ! in structural homology relationship with -disjoint_from: RO:HOM0000062 ! in equivalogy relationship with - -[Typedef] -id: RO:HOM0000017 -name: in orthology relationship with -def: "Historical homology that involves genes that diverged after a speciation event." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000017, http://www.ncbi.nlm.nih.gov/pubmed/5449325] -synonym: "orthologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000018 -name: in xenology relationship with -def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000018] -synonym: "xenologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000019 -name: in 1 to 1 homology relationship with -def: "Historical homology that involves two members sharing no other homologs in the lineages considered." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000019] -synonym: "1 to 1 homologous to" EXACT [] -synonym: "1:1 homology" EXACT [] -synonym: "one-to-one homology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000020 -name: in 1 to 1 orthology relationship with -def: "Orthology that involves two genes that did not experience any duplication after the speciation event that created them." [http://dx.doi.org/10.1007/BF02814484, http://purl.obolibrary.org/obo/HOM_0000020, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "1 to 1 orthologous to" EXACT [] -synonym: "1:1 orthology" EXACT [] -synonym: "one-to-one orthology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000017 ! in orthology relationship with -is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with - -[Typedef] -id: RO:HOM0000022 -name: in ohnology relationship with -def: "Paralogy that results from a whole genome duplication event." [http://dx.doi.org/10.1038/75560, http://purl.obolibrary.org/obo/HOM_0000022] -synonym: "homoeology" RELATED [] -synonym: "ohnologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000023 -name: in in-paralogy relationship with -def: "Paralogy that results from a lineage-specific duplication subsequent to a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000023] -synonym: "in-paralogous to" EXACT [] -synonym: "inparalogy" EXACT [] -synonym: "symparalogy" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with -disjoint_from: RO:HOM0000024 ! in out-paralogy relationship with - -[Typedef] -id: RO:HOM0000024 -name: in out-paralogy relationship with -def: "Paralogy that results from a duplication preceding a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000024] -synonym: "alloparalogy" EXACT [] -synonym: "out-paralogous to" EXACT [] -synonym: "outparalogy" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000025 -name: in pro-orthology relationship with -def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] -synonym: "pro-orthologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000034 ! in 1 to many orthology relationship with - -[Typedef] -id: RO:HOM0000026 -name: in semi-orthology relationship with -def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000026] -synonym: "semi-orthologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000034 ! in 1 to many orthology relationship with - -[Typedef] -id: RO:HOM0000027 -name: in serial homology relationship with -def: "Iterative homology that involves structures arranged along the main body axis." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000027] -synonym: "homonomy" RELATED [] -synonym: "serial homologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000066 ! in iterative homology relationship with - -[Typedef] -id: RO:HOM0000028 -name: in heterochronous homology relationship with -def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [http://purl.obolibrary.org/obo/HOM_0000028, ISBN:978-0674639416] -synonym: "heterochronous homologous to" EXACT [] -synonym: "heterochrony" EXACT [] -is_symmetric: true -is_a: RO:HOM0000008 ! in biological homology relationship with - -[Typedef] -id: RO:HOM0000029 -name: in paedomorphorsis relationship with -def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000029, ISBN:978-0674639416] -synonym: "juvenification" EXACT [] -synonym: "pedomorphosis" EXACT [] -is_symmetric: true -is_a: RO:HOM0000028 ! in heterochronous homology relationship with -disjoint_from: RO:HOM0000030 ! in peramorphosis relationship with - -[Typedef] -id: RO:HOM0000030 -name: in peramorphosis relationship with -def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] -is_symmetric: true -is_a: RO:HOM0000028 ! in heterochronous homology relationship with - -[Typedef] -id: RO:HOM0000031 -name: in progenesis relationship with -def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] -is_symmetric: true -is_a: RO:HOM0000029 ! in paedomorphorsis relationship with - -[Typedef] -id: RO:HOM0000032 -name: in neoteny relationship with -def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, http://purl.obolibrary.org/obo/HOM_0000032, ISBN:978-0674639416] -synonym: "juvenilization" EXACT [] -synonym: "neotenous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000029 ! in paedomorphorsis relationship with - -[Typedef] -id: RO:HOM0000033 -name: in mimicry relationship with -def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033] -synonym: "mimicrous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000004 ! in convergence relationship with - -[Typedef] -id: RO:HOM0000034 -name: in 1 to many orthology relationship with -def: "Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000034, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "1 to many orthologous to" EXACT [] -synonym: "1:many orthology" EXACT [] -synonym: "co-orthology" RELATED [] -synonym: "many to 1 orthology" RELATED [] -synonym: "one-to-many orthology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000017 ! in orthology relationship with -is_a: RO:HOM0000037 ! in 1 to many homology relationship with - -[Typedef] -id: RO:HOM0000036 -name: in many to many homology relationship with -def: "Historical homology that involves two members of a larger set of homologs." [http://dx.doi.org/10.1093/molbev/msp002, http://purl.obolibrary.org/obo/HOM_0000036] -synonym: "many to many homologous to" EXACT [] -synonym: "many-to-many homology" EXACT [] -synonym: "many:many homology " EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000037 -name: in 1 to many homology relationship with -def: "Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000037] -synonym: "1 to many homologous to" EXACT [] -synonym: "1:many homology" RELATED [] -synonym: "one-to-many homology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000042 -name: in apomorphy relationship with -def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [http://purl.obolibrary.org/obo/HOM_0000042, ISBN:978-0252068140] -synonym: "apomorphous to" EXACT [] -synonym: "synapomorphy" RELATED [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with -disjoint_from: RO:HOM0000043 ! in plesiomorphy relationship with - -[Typedef] -id: RO:HOM0000043 -name: in plesiomorphy relationship with -def: "Historical homology that is based on distant shared ancestry." [http://purl.obolibrary.org/obo/HOM_0000043, ISBN:978-0252068140] -synonym: "plesiomorphous to" EXACT [] -synonym: "symplesiomorphy" RELATED [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000044 -name: in deep homology relationship with -def: "Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1038/nature07891, http://purl.obolibrary.org/obo/HOM_0000044] -synonym: "deep genetic homology" EXACT [] -synonym: "deep homologous to" EXACT [] -synonym: "generative homology" RELATED [] -synonym: "homoiology" RELATED [] -is_symmetric: true -is_a: RO:HOM0000003 ! in homocracy relationship with -is_a: RO:HOM0000005 ! in parallelism relationship with - -[Typedef] -id: RO:HOM0000045 -name: in hemiplasy relationship with -def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] -synonym: "hemiplasous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000046 -name: in gametology relationship with -def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] -synonym: "gametologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000047 ! in chromosomal homology relationship with - -[Typedef] -id: RO:HOM0000047 -name: in chromosomal homology relationship with -def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [http://purl.obolibrary.org/obo/HOM_0000047, ISBN:0195307615] -synonym: "chromosomal homologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000048 -name: in many to many orthology relationship with -def: "Orthology that involves two genes that experienced duplications more recent than the species split that created them." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000048, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "co-orthology" RELATED [] -synonym: "many to many orthologous to" EXACT [] -synonym: "many-to-many orthology" EXACT [] -synonym: "many:many orthology" EXACT [] -synonym: "trans-homology" RELATED [] -synonym: "trans-orthology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000017 ! in orthology relationship with -is_a: RO:HOM0000036 ! in many to many homology relationship with - -[Typedef] -id: RO:HOM0000049 -name: in within-species paralogy relationship with -def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "within-species paralogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with -disjoint_from: RO:HOM0000050 ! in between-species paralogy relationship with - -[Typedef] -id: RO:HOM0000050 -name: in between-species paralogy relationship with -def: "Paralogy that involves genes from different species." [http://purl.obolibrary.org/obo/HOM_0000050, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "between-species paralogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000051 -name: in postdisplacement relationship with -def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] -synonym: "post-displacement" EXACT [] -is_symmetric: true -is_a: RO:HOM0000029 ! in paedomorphorsis relationship with - -[Typedef] -id: RO:HOM0000052 -name: in hypermorphosis relationship with -def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] -is_symmetric: true -is_a: RO:HOM0000030 ! in peramorphosis relationship with - -[Typedef] -id: RO:HOM0000053 -name: in synology relationship with -def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] -synonym: "synologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000018 ! in xenology relationship with - -[Typedef] -id: RO:HOM0000054 -name: in isoorthology relationship with -def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000054] -synonym: "isoorthologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000017 ! in orthology relationship with -is_a: RO:HOM0000062 ! in equivalogy relationship with - -[Typedef] -id: RO:HOM0000055 -name: in tandem paralogy relationship with -def: "Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000055, ISBN:978-0878932665] -synonym: "iterative paralogy" RELATED [] -synonym: "serial paralogy" RELATED [] -synonym: "tandem paralogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000057 -name: in latent homology relationship with -def: "Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character)." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000057, ISBN:0199141118] -synonym: "apomorphic tendency" EXACT [] -synonym: "cryptic homology" EXACT [] -synonym: "homoiology" RELATED [] -synonym: "homoplastic tendency" RELATED [] -synonym: "latent homologous to" EXACT [] -synonym: "re-awakening" RELATED [] -synonym: "underlying synapomorphy" EXACT [] -is_symmetric: true -is_a: RO:HOM0000005 ! in parallelism relationship with -is_a: RO:HOM0000058 ! in syngeny relationship with - -[Typedef] -id: RO:HOM0000058 -name: in syngeny relationship with -def: "Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual." [DOI:10.1002/1521-1878(200009)22\:9<846\:\:AID-BIES10>3.0.CO;2-R, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000058] -synonym: "generative homology" EXACT [] -synonym: "syngenous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000003 ! in homocracy relationship with - -[Typedef] -id: RO:HOM0000060 -name: in apparent orthology relationship with -def: "Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000060, http://www.ensembl.org/info/docs/compara/homology_method.html] -synonym: "1:1 paralogy" EXACT [] -synonym: "apparent 1:1 orthology" EXACT [] -synonym: "apparent orthologous to" EXACT [] -synonym: "pseudoorthology" EXACT [] -is_symmetric: true -is_a: RO:HOM0000019 ! in 1 to 1 homology relationship with -is_a: RO:HOM0000050 ! in between-species paralogy relationship with - -[Typedef] -id: RO:HOM0000061 -name: in pseudoparalogy relationship with -def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000061] -synonym: "pseudoparalogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000018 ! in xenology relationship with - -[Typedef] -id: RO:HOM0000062 -name: in equivalogy relationship with -def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1093/nar/gkl1043, http://purl.obolibrary.org/obo/HOM_0000062] -synonym: "equivalogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with -is_a: RO:HOM0000065 ! in functional equivalence relationship with - -[Typedef] -id: RO:HOM0000063 -name: in interology relationship with -def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] -synonym: "interologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - -[Typedef] -id: RO:HOM0000065 -name: in functional equivalence relationship with -def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] -synonym: "functional similarity" RELATED [] -is_symmetric: true -is_a: RO:HOM0000000 ! in similarity relationship with - -[Typedef] -id: RO:HOM0000066 -name: in iterative homology relationship with -def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] -synonym: "iterative homologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000008 ! in biological homology relationship with - -[Typedef] -id: RO:HOM0000068 -name: in paraxenology relationship with -def: "Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome." [http://purl.obolibrary.org/obo/HOM_0000068, http://www.ncbi.nlm.nih.gov/pubmed/3065587] -synonym: "duplicate xenology" EXACT [] -synonym: "multiple xenology" EXACT [] -synonym: "paraxenologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000018 ! in xenology relationship with - -[Typedef] -id: RO:HOM0000069 -name: in plerology relationship with -def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [http://purl.obolibrary.org/obo/HOM_0000069, http://www.ncbi.nlm.nih.gov/pubmed/3065587] -synonym: "plerologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000011 ! in paralogy relationship with - -[Typedef] -id: RO:HOM0000071 -name: in homotopy relationship with -def: "Structural homology that involves structures with the same or similar relative positions." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/BF02814485, http://purl.obolibrary.org/obo/HOM_0000071, ISBN:0123195837] -synonym: "homotopous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000006 ! in structural homology relationship with -disjoint_from: RO:HOM0000072 ! in homeosis relationship with - -[Typedef] -id: RO:HOM0000072 -name: in homeosis relationship with -def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] -synonym: "heterotopy" RELATED [] -is_symmetric: true -is_a: RO:HOM0000008 ! in biological homology relationship with - -[Typedef] -id: RO:HOM0000073 -name: in homoeology relationship with -def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pnas.0505156102, http://purl.obolibrary.org/obo/HOM_0000073] -synonym: "homoeologous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000022 ! in ohnology relationship with -is_a: RO:HOM0000053 ! in synology relationship with - -[Typedef] -id: RO:HOM0000074 -name: in paramorphism relationship with -def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] -synonym: "axis paramorphism" RELATED [] -is_symmetric: true -is_a: RO:HOM0000003 ! in homocracy relationship with -is_a: RO:HOM0000066 ! in iterative homology relationship with - -[Typedef] -id: RO:HOM0000075 -name: in regulogy relationship with -def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] -synonym: "regulogous to" EXACT [] -is_symmetric: true -is_a: RO:HOM0000007 ! in historical homology relationship with - diff --git a/src/ontology/subsets/ro-chado.owl b/src/ontology/subsets/ro-chado.owl new file mode 100644 index 00000000..23ffa7b2 --- /dev/null +++ b/src/ontology/subsets/ro-chado.owl @@ -0,0 +1,12379 @@ + + + + + 2023-02-19 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + + + + + + + + + + OBO foundry unique label + + + + + + + + + + + + + + + + + + + + + term replaced by + + + + + + + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + defined by construct + + + + + + + + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + temporal interpretation + + + + + + + + + + tooth SubClassOf 'never in taxon' value 'Aves' + x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. + + + + Class: ?X DisjointWith: RO_0002162 some ?Y + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> +PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> +CONSTRUCT { + in_taxon: a owl:ObjectProperty . + ?x owl:disjointWith [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom ?taxon + ] . + ?x rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom [ + a owl:Class ; + owl:complementOf ?taxon + ] + ] . +} +WHERE { + ?x never_in_taxon: ?taxon . +} + never in taxon + + + + + + + + + + A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. + non-overlapping with + shares no parts with + + Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) + PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> +PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> +CONSTRUCT { + part_of: a owl:ObjectProperty . + [ + a owl:Restriction ; + owl:onProperty part_of: ; + owl:someValuesFrom ?x ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty part_of: ; + owl:someValuesFrom ?y + ] + ] +} +WHERE { + ?x mutually_spatially_disjoint_with: ?y . +} + mutually spatially disjoint with + + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + + + + + + + + + An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. + taxonomic class assertion + + + + + + + + + + S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] + ambiguous for taxon + + + + + + + + + + S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. + + + This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost + dubious for taxon + + + + + + + + + + S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S + + + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> +PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> +CONSTRUCT { + in_taxon: a owl:ObjectProperty . + ?witness rdfs:label ?label . + ?witness rdfs:subClassOf ?x . + ?witness rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom ?taxon + ] . +} +WHERE { + ?x present_in_taxon: ?taxon . + BIND(IRI(CONCAT( + "http://purl.obolibrary.org/obo/RO_0002175#", + MD5(STR(?x)), + "-", + MD5(STR(?taxon)) + )) as ?witness) + BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) +} + The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. + present in taxon + + + + + + + + + + defined by inverse + + + + + + + + + An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. + logical macro assertion + http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ + + + + + + + + An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. + annotation property cardinality + + + + + + + + + + A logical macro assertion whose domain is an IRI for a class + The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL + logical macro assertion on a class + + + + + + + + + A logical macro assertion whose domain is an IRI for a property + logical macro assertion on a property + + + + + + + + + Used to annotate object properties to describe a logical meta-property or characteristic of the object property. + logical macro assertion on an object property + + + + + + + + + logical macro assertion on an annotation property + + + + + + + + + An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. + dispositional interpretation + + + + + + + + + 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' + A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. + shares no connection with + Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) + has no connections with + + + + + + + + + inherited annotation property + + + + + + + + Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) + curator guidance link + + + + + + + + + brain always_present_in_taxon 'Vertebrata' + forelimb always_present_in_taxon Euarchontoglires + S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S + This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. + never lost in + always present in taxon + + + + + + + + + This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. + temporal logical macro assertion on a class + + + + + + + + + measurement property has unit + + + + + + + + + has start time value + + + + + + + + + + has end time value + + + + + + + + + + Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. + start, days post fertilization + + + + + + + + + + Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. + end, days post fertilization + + + + + + + + + + Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. + start, years post birth + + + + + + + + + + Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 + end, years post birth + + + + + + + + + + Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. + start, months post birth + + + + + + + + + + Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 + end, months post birth + + + + + + + + + + Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. + month of gestation + + + + + + + + + + A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process + has developmental stage marker + + + + + + + + + + Count of number of days intervening between the start of the stage and the time of coitum. + For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) + start, days post coitum + + + + + + + + + + Count of number of days intervening between the end of the stage and the time of coitum. + end, days post coitum + + + + + + + + + + start, weeks post birth + + + + + + + + + + end, weeks post birth + + + + + + + + + + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p + is asymmetric relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p + is symmetric relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process + is relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y + The general property hierarchy is: + + "directly P" SubPropertyOf "P" + Transitive(P) + +Where we have an annotation assertion + + "directly P" "is direct form of" "P" + If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' + + is direct form of + + + + + + + + + + relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y + + is indirect form of + + + + + + + + + + logical macro assertion on an axiom + + + + + + + + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom + + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. + is relational form of a class + + + + + + + + + A shortcut relationship that holds between two entities based on their identity criteria + logical macro assertion involving identity + + + + + + + + + A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. + in approximate one to one relationship with + + + + + + + + + x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y + The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" + is approximately equivalent to + + + + + + + + + 'anterior end of organism' is-opposite-of 'posterior end of organism' + 'increase in temperature' is-opposite-of 'decrease in temperature' + x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + is opposite of + + + + + + + + + x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + is indistinguishable from + + + + + + + + + evidential logical macro assertion on an axiom + + + + + + + + + A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom has evidence + + + + + + + + + A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom contradicted by evidence + + + + + + + + + In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. + this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. + If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion + is representative IRI for equivalence set + OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member + + + + + + + + + true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. + + nominally disjoint with + + + + + + + + + Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" + + 2018-03-13T23:59:29Z + is directional form of + + + + + + + + + + 2018-03-14T00:03:16Z + is positive form of + + + + + + + + + + 2018-03-14T00:03:24Z + is negative form of + + + + + + + + + part-of is homeomorphic for independent continuants. + R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. + + 2018-10-21T19:46:34Z + R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. + is homeomorphic for + + + + + + + + + + pg + 2020-09-22T11:05:29Z + valid_for_go_annotation_extension + + + + + + + + + + pg + 2020-09-22T11:05:18Z + valid_for_go_gp2term + + + + + + + + + + pg + 2020-09-22T11:04:12Z + valid_for_go_ontology + + + + + + + + + + pg + 2020-09-22T11:05:45Z + valid_for_gocam + + + + + + + + + + eco subset + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subset_property + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_broad_synonym + + + + + + + + database_cross_reference + + + + + + + + has_exact_synonym + + + + + + + + has_narrow_synonym + + + + + + + + has_obo_format_version + + + + + + + + has_related_synonym + + + + + + + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + is defined by + + + + + is defined by + This is an experimental annotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + + + + + + + + + + + + part of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + + + + has part + + + + + + + + + realized in + this disease is realized in this disease course + this fragility is realized in this shattering + this investigator role is realized in this investigation + is realized by + realized_in + [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + realizes + this disease course realizes this disease + this investigation realizes this investigator role + this shattering realizes this fragility + to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + accidentally included in BFO 1.2 proposal + - should have been BFO_0000062 + obsolete preceded by + true + + + + + + + + + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by + + + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in + + + + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity. + derives from part of + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + has characteristic + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + + + + + + + OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete in neural circuit with + true + + + + + + + + + + OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete upstream in neural circuit with + true + + + + + + + + + + OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete downstream in neural circuit with + true + + + + + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + + derives from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + + derives into + + + + + + + + + + is location of + my head is the location of my brain + this cage is the location of this rat + a relation between two independent continuants, the location and the target, in which the target is entirely within the location + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + location_of + + location of + + + + + + + + + + + + + contained in + Containment is location not involving parthood, and arises only where some immaterial continuant is involved. + Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): + Intended meaning: +domain: material entity +range: spatial region or site (immaterial continuant) + + contained_in + + + contained in + + + + + + + + contains + + + contains + + + + + + + + + + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is allergic trigger for + + + + + + + + + + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is autoimmune trigger for + + + + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has allergic trigger + + + + + + + + + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has autoimmune trigger + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in + + located in + + + + + + + + + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of + surface of + + 2D boundary of + + + + + + + + + + May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 + + + aligned with + + + + + + + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + + has boundary + has_2D_boundary + + has 2D boundary + + + + + + + + + A relation that holds between two neurons that are electrically coupled via gap junctions. + + + electrically_synapsed_to + + + + + + + + + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + + tracheates + + + + + + + + + + http://www.ncbi.nlm.nih.gov/pubmed/22402613 + innervated_by + + + + + + + + + + + + has synaptic terminal of + + + + + + + + + X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. + bounding layer of + + + + + + + + + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + Note from NCEAS meeting: consider changing primary label + + + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. + coincident with + + + + + + + + + A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. + + x 'cell expresses' y iff: +cell(x) +AND gene(y) +AND exists some 'transcription, DNA templated (GO_0006351)'(t) +AND t occurs_in x +AND t has_input y + cell expresses + + + + + + + + + x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + regulates in other organism + + + + + + + + + + + + A relationship that holds between a process that regulates a transport process and the entity transported by that process. + + + regulates transport of + + + + + + + + + + A part of relation that applies only between occurrents. + occurrent part of + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + dos + 2017-07-19T17:30:36Z + has ligand + + + + + + + + + Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. + dos + 2017-07-20T17:11:08Z + transports + + + + + + + + + A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. + dos + 2017-07-20T17:19:37Z + occurs across + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + A relationship that holds between two images, A and B, where: +A depicts X; +B depicts Y; +X and Y are both of type T' +C is a 2 layer image consiting of layers A and B; +A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. +Note: A and B may be 2D or 3D. +Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. + dos + 2017-12-07T12:58:06Z + in register with + + + + + A relationship that holds between two images, A and B, where: +A depicts X; +B depicts Y; +X and Y are both of type T' +C is a 2 layer image consiting of layers A and B; +A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. +Note: A and B may be 2D or 3D. +Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. + GOC:dos + + + + + + + + + David Osumi-Sutherland + <= + + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + + + + + David Osumi-Sutherland + + starts before + + + + + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + David Osumi-Sutherland + io + + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + + + + + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + + + + + + + + + + + + + + Relation between a neuron and an anatomical structure that its soma is part of. + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) + + has soma location + + + + + + + + + + + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. + + + fasciculates with + (forall (?x ?y) + (iff + (fasciculates_with ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron ; CL_0000540" ?x) + ("neuron projection bundle ; CARO_0001001" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500' " ?npbs) + (part_of ?npbs ?y) + (part_of ?nps ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + + fasciculates with + + + + + + + + + + + + + + Relation between a neuron and some structure its axon forms (chemical) synapses in. + + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( + <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) + + + axon synapses in + + + + + + + + + + + Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + synapsed by + + + + + + + + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] + + Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. + + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) + + has plasma membrane part + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. + + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_Ib_bouton_to + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. + + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_Is_bouton_to + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type II bouton. + + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_II_bouton_to + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type II bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_II_bouton + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_Ib_bouton + + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + + + synapsed in + http://purl.obolibrary.org/obo/BFO_0000051 some ( + http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( + http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) + + + has postsynaptic terminal in + + + + + + + + + has neurotransmitter + releases neurotransmitter + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_Is_bouton + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + synapses in + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) + + + has presynaptic terminal in + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type III bouton. + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_III_bouton_to + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type III bouton. + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_III_bouton + + + + + + + + + + Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + N1 synapsed_to some N2 +Expands to: +N1 SubclassOf ( + has_part some ( + ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( + ‘synapse ; GO:0045202’ that has_part some ( + ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) + synapsed to + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. + + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( + http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( + <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) + + + dendrite synapsed in + + + + + + + + + + + + + + A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. + + has synapse in + <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) + + + has synaptic terminal in + + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + + + overlaps + + + + + + + + + true + + + + + + + + + + The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. + + has fasciculating component + (forall (?x ?y) + (iff + (has_fasciculating_neuron_projection ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron projection bundle ; CARO_0001001" ?x) + ("neuron projection ; GO0043005" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500" ?npbs) + (part_of ?nps ?y) + (part_of ?npbs ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + + + + + has fasciculating neuron projection + + + + + + + + + + + + + Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. +T innervates some R +Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + innervates + + + + + + + + + + + X continuous_with Y if and only if X and Y share a fiat boundary. + + connected to + The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) + + continuous with + FMA:85972 + + + + + + + + + + x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x + We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom + proper overlaps + (forall (?x ?y) + (iff + (proper_overlaps ?x ?y) + (and + (overlaps ?x ?y) + (not (part_of ?x ?y)) + (not (part_of ?y ?x))))) + + + partially overlaps + + + + + + + + + + + + d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + ancestral_stucture_of + evolutionarily_descended_from + derived by descent from + + + + + + + + + + + inverse of derived by descent from + + has derived by descendant + + + + + + + + + + + + + + + + two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + Consider obsoleting and merging with child relation, 'in homology relationship with' + VBO calls this homologous_to + shares ancestor with + + + + + + + + + + + + serially homologous to + + + + + + + + + lactation SubClassOf 'only in taxon' some 'Mammalia' + + x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. + + 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria + + + + only in taxon + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + + + + + + Connects a biological entity to its taxon of origin. + in taxon + + + + + + + + + + + A is spatially_disjoint_from B if and only if they have no parts in common + There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. + + + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy + BFO_0000051 exactly 0 (BFO_0000050 some ?Y) + + + spatially disjoint from + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + + + + + + + + + + + + + + + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b + + connected to + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + + + + + + + + + The M8 connects Glasgow and Edinburgh + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. + + connects + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + + + + + + + + + + + + + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) + attached to part of + + + + + + + + + true + + + + + + + + + Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. + Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure + + supplies + + + + + + + + + Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. + Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure + + drains + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component + + + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + + + has phenotype + + + + + + + + + + inverse of has phenotype + + + + phenotype of + + + + + + + + + + + + x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + + + + + This is the transitive form of the develops from relation + develops from + + + + + + + + + + + + + inverse of develops from + + + + + develops into + + + + + + + + + + + + + + + definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" + We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. + + gene product of + + + + + + + + + + + + + every HOTAIR lncRNA is the gene product of some HOXC gene + every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene + + x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y + + has gene product + + + + + + + + + + + + + + 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' + + x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process + + expressed in + + + + + + + + + + + Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. + + + FBbt + + has developmental precursor + TODO - add child relations from DOS + directly develops from + + + + + + + + + + A parasite that kills or sterilizes its host + parasitoid of + + + + + + + + + inverse of parasitoid of + + has parasitoid + + + + + + + + + + inverse of directly develops from + developmental precursor of + + directly develops into + + + + + + + + + + + + + + + + + + + + + + + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. + + + + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + + + + regulates + + + + + + + + + + + + + + + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. + + + negatively regulates (process to process) + + + + + negatively regulates + + + + + + + + + + + + + + + + + + + + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. + + + positively regulates (process to process) + + + + + positively regulates + + + + + + + + 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) + heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') + + x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. + Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + TODO: add homeomorphy axiom + This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. + + has prototype + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + + capable of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + + has function in + capable of part of + + + + + + + + + + true + + + + + + + + OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role + + agent in + + Obsoleted as the inverse property was obsoleted. + obsolete actively participates in + true + + + + + + + + OBSOLETE x has participant y if and only if x realizes some active role that inheres in y + + has agent + + obsolete has active participant + true + + + + + + + + + + + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x + + + surrounded by + + + + + + + + + A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. + The epidermis layer of a vertebrate is adjacent to the dermis. + The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. + The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. + + x adjacent to y if and only if x and y share a boundary. + This relation acts as a join point with BSPO + + + + + + adjacent to + + + + + A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. + + + + + + + + + + + inverse of surrounded by + + + + surrounds + + + + + + + + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + inverse of starts with + + Chris Mungall + Allen + + starts + + + + + + + + + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + started by + + starts with + + + + + + + + + + + + + + x develops from part of y if and only if there exists some z such that x develops from z and z is part of y + + develops from part of + + + + + + + + + + + + + + x develops_in y if x is located in y whilst x is developing + + EHDAA2 + Jonathan Bard, EHDAA2 + develops in + + + + + + + + + A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. + obligate parasite of + + + + + + + + + A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. + facultative parasite of + + + + + + + + + + + + inverse of ends with + + Chris Mungall + + ends + + + + + + + + + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + finished by + + ends with + + + + + + + + + + + + + + x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + + starts with process that occurs in + + has start location + + + + + + + + + + + + + + x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + + ends with process that occurs in + + has end location + + + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + consumes + + + + + has input + + + + + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + + produces + + + + + has output + + + + + + + + + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) + stem parasite of + + + + + + + + + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) + root parasite of + + + + + + + + + A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. + hemiparasite of + + + + + + + + + X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. + + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). + +If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + has component participant + + + + + + + + + A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. + ExO:0000001 + has exposure receptor + + + + + + + + + A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. + ExO:0000000 + has exposure stressor + + + + + + + + + A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor + ExO:0000055 + has exposure route + + + + + + + + + A broad relationship between an exposure event or process and the course takes from the source to the target. + http://purl.obolibrary.org/obo/ExO_0000004 + has exposure transport path + + + + + + + + + Any relationship between an exposure event or process and any other entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. + related via exposure to + + + + + + + + + g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. + over-expressed in + + + + + + + + + g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. + under-expressed in + + + + + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. + has active substance + has active pharmaceutical ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + + active ingredient in + + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. + b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. + + connecting branch of + + + + + + + + + + inverse of connecting branch of + + + has connecting branch + + + + + + + + + + + + + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] + + x has developmental contribution from y iff x has some part z such that z develops from y + + has developmental contribution from + + + + + + + + + + + + + + + inverse of has developmental contribution from + + + developmentally contributes to + + + + + + + + + + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T + + + + induced by + + Developmental Biology, Gilbert, 8th edition, figure 6.5(F) + GO:0001759 + We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] + developmentally induced by + + + + + + + + + + + Inverse of developmentally induced by + + developmentally induces + + + + + + + + + + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + false + + In general you should not use this relation to make assertions - use one of the more specific relations below this one + This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from + developmentally preceded by + + + + + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + has chemical role + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + + acts upstream of or within + + + + + + + + + + + x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else + This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage + + replaces + developmentally replaces + + + + + + + + + + Inverse of developmentally preceded by + + developmentally succeeded by + + + + + + + + + + + + + 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue + + + part of developmental precursor of + + + + + + + + + + + x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x + Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. + + ubiquitously expressed in + + + + + + + + + + Inverse of 'expressed in' + + expresses + + + + + + + + + + inverse of ubiquiotously expressed in + + + ubiquitously expresses + + + + + + + + + + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). + This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. + + results in developmental progression of + + + + + + + + + + + every flower development (GO:0009908) results in development of some flower (PO:0009046) + + p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. + + http://www.geneontology.org/GO.doc.development.shtml + + + + results in development of + + + + + + + + + + + an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. + every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + + + GOC:mtg_berkeley_2013 + + + + results in formation of + + + + + + + + + + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. + tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) + + The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. + + GOC:mtg_berkeley_2013 + + + + results in morphogenesis of + + + + + + + + + + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process + bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) + + The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + + GOC:mtg_berkeley_2013 + + + + results in maturation of + + + + + + + + + foramen ovale closure SubClassOf results in disappearance of foramen ovale + + + May be merged into parent relation + results in disappearance of + + + + + + + + + every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) + + + May be merged into parent relation + results in developmental regression of + + + + + + + + + + Inverse of 'is substance that treats' + + + is treated by substance + + + + + + + + + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' +where +'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview + + x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. + + adapted for living in + + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. + has habitat + + + + + + + + + + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. + + + + + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. + + + + + causally upstream of, negative effect + + + + + + + + + A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. + + + + + 2017-06-05T17:35:04Z + has exposure stimulus + + + + + + + + + + evolutionary variant of + + + + + + + + + + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. + + regulates localization of + + + + transports or maintains localization of + + + + + + + + + + + + + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + characteristic of part of + + + + + + + + + + true + + + + + + + + + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. + The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity + + GOC:mtg_berkeley_2013 + + + + results in acquisition of features of + + + + + + + + A relationship that holds via some environmental process + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + evolutionarily related to + + + + + + + + A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + + ecologically related to + + + + + + + + + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. + + adapted for + + confers advantage in + + + + + + + + A mereological relationship or a topological relationship + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to + + + + + + + + A relationship that holds between entities participating in some developmental process (GO:0032502) + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development + developmentally related to + + + + + + + + + Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) + a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. + + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] + + colocalizes with + + + + + + + + + + ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. + Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. + eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex + We would like to say + +if and only if + exists c', p' + c part_of c' and c' capable_of p + and + c capable_of p' and p' part_of p +then + c contributes_to p + +However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. + + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + + contributes to + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. + + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + + This is a grouping relation that collects relations used for the purpose of connecting structure and function + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + + false + part of structure that is capable of + + + + + + + + + true + + + + + + + + holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism + genomically related to + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + + actively involved in + enables part of + involved in + + + + + + + + + + every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid + p regulates levels of c if p regulates some amount (PATO:0000070) of c + + + regulates levels of (process to entity) + regulates levels of + + + + + + + + + + inverse of enables + + + enabled by + + + + + + + + + + inverse of regulates + + regulated by (processual) + + regulated by + + + + + + + + + inverse of negatively regulates + + + negatively regulated by + + + + + + + + + inverse of positively regulates + + + positively regulated by + + + + + + + + A relationship that holds via some process of localization + + Do not use this relation directly. It is a grouping relation. + related via localization to + + + + + + + + + + + + + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. + + + + + has target start location + + + + + + + + + + + + + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. + + + + + has target end location + + + + + + + + + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. + + + imports + + + + + + + + + Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l + + results in transport along + + + + + + + + + + Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. + + + results in transport across + + + + + + + + + + 'pollen tube growth' results_in growth_of some 'pollen tube' + + results in growth of + + + + + + + + + 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) + + results in transport to from or in + + + + + + + + + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + + + exports + + + + + + + + + an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. + p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. + + + + + results in commitment to + + + + + + + + + p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. + + + + + results in determination of + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + inverse of has input + + + + input of + + + + + + + + + + inverse of has output + + + + output of + + + + + + + + + + formed as result of + + + + + + + + + + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. + + results in structural organization of + + + + + + + + + The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. + + + + + results in specification of + + + + + + + + + p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. + + results in developmental induction of + + + + + + + + + + http://neurolex.org/wiki/Property:DendriteLocation + has dendrite location + + + + + + + + + + + a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a + + attached to (anatomical structure to anatomical structure) + + attached to + + + + + + + + + + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. + + Wikipedia:Insertion_(anatomy) + has muscle origin + + + + + + + + + + + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + + Wikipedia:Insertion_(anatomy) + has muscle insertion + + + + + + + + + + false + + x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat + + + has fused element + A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. + derived from ancestral fusion of + + + + + + + + + + A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) + + in branching relationship with + + https://github.com/obophenotype/uberon/issues/170 + + + + + + + + + + Deschutes River tributary_of Columbia River + inferior epigastric vein tributary_of external iliac vein + + x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. + + drains into + drains to + tributary channel of + http://en.wikipedia.org/wiki/Tributary + http://www.medindia.net/glossary/venous_tributary.htm + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) + + tributary of + + http://en.wikipedia.org/wiki/Tributary + + + + + + + + + + Deschutes River distributary_of Little Lava Lake + + x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x + + branch of + distributary channel of + http://en.wikipedia.org/wiki/Distributary + + This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes + distributary of + + + + + + + + + + + + + + + + + x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. + + anastomoses with + + anabranch of + + + + + + + + + + + + + + + A lump of clay and a statue + x spatially_coextensive_with y if and inly if x and y have the same location + + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios + spatially coextensive with + + + + + + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S + x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y + + + branching part of + + FMA:85994 + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. + + x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. + + + main stem of + + + + + + + + + + + x proper_distributary_of y iff x distributary_of y and x does not flow back into y + + + proper distributary of + + + + + + + + + + x proper_tributary_of y iff x tributary_of y and x does not originate from y + + + proper tributary of + + + + + + + + + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + + has developmental potential involving + + + + + + + + + + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + + has potential to developmentally contribute to + + + + + + + + + + x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y + + has potential to developmentally induce + + + + + + + + + + x has the potential to develop into y iff x develops into y or if x is capable of developing into y + + has potential to develop into + + + + + + + + + + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + + has potential to directly develop into + + + + + + + + + + + + + 'protein catabolic process' SubClassOf has_direct_input some protein + + p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + directly consumes + This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' + has direct input + + + + + + + + + + Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + obsolete has indirect input + true + + + + + + + + translation SubClassOf has_direct_output some protein + + p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. + + directly produces + obsolete has direct output + true + + + + + + + + + + + + + + Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + obsolete has indirect output + true + + + + + + + + + + + + inverse of upstream of + + causally downstream of + + + + + + + + + + + + + immediately causally downstream of + + + + + + + + + This term was obsoleted because it has the same meaning as 'directly positively regulates'. + obsolete directly activates + true + + + + + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + + indirectly activates + + indirectly positively regulates + + + + + + + + + This term was obsoleted because it has the same meaning as 'directly negatively regulates'. + obsolete directly inhibits + true + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + + indirectly inhibits + + indirectly negatively regulates + + + + + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative? + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types. + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causally related to + + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + + + + + + + + + + + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. + + + + causally upstream of + + + + + + + + + + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. + + + immediately causally upstream of + + + + + + + + + + + + + + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. + This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit + + directly provides input for + + directly provides input for (process to process) + provides input for + + + + + + + + + + + transitive form of directly_provides_input_for + + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. + transitively provides input for (process to process) + transitively provides input for + + + + + + + + + + + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + + influences (processual) + affects + causally upstream of or within + + + + + + + + false + + This is an exploratory relation + differs in + https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions + + + + + + + + + + differs in attribute of + + + + + + + + + + differs in attribute + + + + + + + + + + inverse of causally upstream of or within + + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + + + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union + + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + + + + A protein that enables activity in a cytosol. + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + + executes activity in + enables activity in + + is active in + + + + + + + + + true + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + + + + + + + + + p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. + + contributes to morphology of + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Considering relabeling as 'pairwise interacts with' + + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 + + + + + + + + + + An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) + + genetically interacts with + + http://purl.obolibrary.org/obo/MI_0208 + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + + + An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. + + interacts with on organism level + + biotically interacts with + + http://eol.org/schema/terms/interactsWith + + + + + + + + + An interaction relationship in which the partners are related via a feeding relationship. + + + trophically interacts with + + + + + + + + + + + A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] + Baleen whale preys on krill + An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members + + + + is subject of predation interaction with + preys upon + + preys on + http://eol.org/schema/terms/preysUpon + http://www.inaturalist.org/observations/2942824 + + + + + + + + + + + + + + + + + A biotic interaction in which the two organisms live together in more or less intimate association. + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism + + symbiotically interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + + commensually interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + + mutualistically interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + This relation groups a pair of inverse relations, parasite of and parasitized by + + interacts with via parasite-host interaction + + + + + + + + + + + + + + + + + + Pediculus humanus capitis parasite of human + + parasitizes + direct parasite of + + parasite of + http://eol.org/schema/terms/parasitizes + + + + + + + + + + + has parasite + parasitised by + directly parasitized by + + parasitized by + http://eol.org/schema/terms/hasParasite + + + + + + + + + Porifiera attaches to substrate + A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. + + semibiotically interacts with + + participates in a abiotic-biotic interaction with + + + + + + + + + + + + + + + Axiomatization to GO to be added later + + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + phosphorylates + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. + + + molecularly controls + directly regulates activity of + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + + + directly inhibits + molecularly decreases activity of + directly negatively regulates activity of + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + + + directly activates + molecularly increases activity of + directly positively regulates activity of + + + + + + + + + all dengue disease transmitted by some mosquito + A relationship that holds between a disease and organism + Add domain and range constraints + + transmitted by + + + + + + + + + A relation that holds between a disease or an organism and a phenotype + + has symptom + + + + + + + + + + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) + + host of + + + + + + + + + X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y + + + has host + http://eol.org/schema/terms/hasHost + + + + + + + + + + Bees pollinate Flowers + This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. + + is subject of pollination interaction with + + pollinates + http://eol.org/schema/terms/pollinates + + + + + + + + + + has polinator + is target of pollination interaction with + + pollinated by + http://eol.org/schema/terms/hasPollinator + + + + + + + + + + + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. + + acquires nutrients from + + + + + + + + + inverse of preys on + + has predator + is target of predation interaction with + + + preyed upon by + http://eol.org/schema/terms/HasPredator + http://polytraits.lifewatchgreece.eu/terms/PRED + + + + + + + + + + Anopheles is a vector for Plasmodium + + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism + + is vector for + + + + + + + + + + + has vector + + + + + + + + + + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + partner in + + + + + + + + + + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + subject participant in + + + + + + + + + + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. + target participant in + + + + + + + + + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + helper property (not for use in curation) + + + + + + + + + + is symbiosis + + + + + + + + + + is commensalism + + + + + + + + + + is mutualism + + + + + + + + + + is parasitism + + + + + + + + + + + provides nutrients for + + + + + + + + + + is subject of eating interaction with + + eats + + + + + + + + + + eaten by + is target of eating interaction with + + is eaten by + + + + + + + + + + A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and +the a supports either the existence of b, or the truth value of b. + + + is evidence for + + + + + + + + + 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' + x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. + + + + + composed primarily of + + + + + + + + + ABal nucleus child nucleus of ABa nucleus (in C elegans) + c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d + + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. + child nucleus of + + + + + + + + + A child nucleus relationship in which the cells are part of a hermaphroditic organism + + child nucleus of in hermaphrodite + + + + + + + + + A child nucleus relationship in which the cells are part of a male organism + + child nucleus of in male + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + + + has part that occurs in + + + + + + + + + true + + + + + + + + + + + + + + An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y + Axiomatization to GO to be added later + + ubiquitinates + + + + + + + + + + is kinase activity + + + + + + + + + + is ubiquitination + + + + + + + + + + See notes for inverse relation + + receives input from + + + + + + + + + This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. + + sends output to + + + + + + + + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. + relation between physical entity and a process or stage + + + + + + + + + + + + + + + + + + x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). + + existence starts during + + + + + + + + + x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). + + existence starts with + + + + + + + + + x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence overlaps + + + + + + + + + + x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + + exists during + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts and ends during + + + + + + + + + + + + + + + + + + x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during + + + + + + + + + x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends with + + + + + + + + + + x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships + + transformation of + + + + + + + + + + x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t + + + immediate transformation of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts during or after + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during or before + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + towards + + + + + + + + + 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate + p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c + + has intermediate product + + has intermediate + + + + + + + + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between entities + + + + + + + + + + + + A coral reef environment is determined by a particular coral reef + s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. + The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future + + + determined by (system to material entity) + + + + determined by + + + + + + + + + inverse of determined by + + determines (material entity to system) + + + determines + + + + + + + + + + + + + + s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. + + + determined by part of + + + + + + + + + true + + + + + + + + + + x is transcribed from y if and only if x is synthesized from template y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + transcribed from + + + + + + + + + inverse of transcribed from + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + transcribed to + + + + + + + + + + x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + ribosomal translation of + + + + + + + + + inverse of ribosomal translation of + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + ribosomally translates to + + + + + + + + A relation that holds between two entities that have the property of being sequences or having sequences. + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. + The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. + + sequentially related to + + + + + + + + + Every UTR is adjacent to a CDS of the same transcript + Two consecutive DNA residues are sequentially adjacent + Two exons on a processed transcript that were previously connected by an intron are adjacent + x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + sequentially adjacent to + + + + + + + + + + + Every CDS has as a start sequence the start codon for that transcript + x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence + + started by + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has start sequence + + + + + + + + + + inverse of has start sequence + + starts + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + + is start sequence of + + + + + + + + + + + Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) + x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence + + ended by + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has end sequence + + + + + + + + + + inverse of has end sequence + + ends + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + + is end sequence of + + + + + + + + + x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. + In the SO paper, this was defined as an instance-type relation + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + is consecutive sequence of + + + + + + + + + + Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. + x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering + + + is sequentially aligned with + + + + + + + + + + + The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) + x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + + + bounds sequence of + + + + + + + + + + inverse of bounds sequence of + + + + is bound by sequence of + + + + + + + + + + + + + x has subsequence y iff all of the sequence parts of y are sequence parts of x + + contains + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has subsequence + + + + + + + + + + + + inverse of has subsequence + + contained by + + + is subsequence of + + + + + + + + + + + + + + + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + + + overlaps sequence of + + + + + + + + + + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + + disconnected from + + does not overlap sequence of + + + + + + + + + + inverse of downstream of sequence of + + + is upstream of sequence of + + + + + + + + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + + + is downstream of sequence of + + + + + + + + + + A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript + x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y + + + + is immediately downstream of sequence of + + + + + + + + + + A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript + inverse of immediately downstream of + + + is immediately upstream of sequence of + + + + + + + + + + + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' + A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. + + has supporting framework + The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). + has skeleton + + + + + + + + + + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. + + results in ending of + + + + + + + + + + + + + + x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y + Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism + + http://eol.org/schema/terms/hyperparasitoidOf + https://en.wikipedia.org/wiki/Hyperparasite + hyperparasitoid of + epiparasite of + + hyperparasite of + + + + + + + + + + + + + inverse of hyperparasite of + + has epiparasite + has hyperparasite + hyperparasitoidized by + + + hyperparasitized by + + + + + + + + + + http://en.wikipedia.org/wiki/Allelopathy + + allelopath of + http://eol.org/schema/terms/allelopathyYes + x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y + + + + + + + + + + + + pathogen of + + + + + + + + + + + has pathogen + + + + + + + + + inverse of is evidence for + + + + + x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. + has evidence + + + + + + + + + + + + causally influenced by (entity-centric) + causally influenced by + + + + + + + + + + interaction relation helper property + + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + + molecular interaction relation helper property + + + + + + + + + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c + + + + + + results in movement of + + + + + + + + + + + + + + + + + + + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). + + + + causally influences (entity-centric) + causally influences + + + + + + + + + A relation that holds between elements of a musculoskeletal system or its analogs. + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. + biomechanically related to + + + + + + + + + m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. + + Wikipedia:Antagonist_(muscle) + has muscle antagonist + + + + + + + + + + + inverse of branching part of + + + + has branching part + + + + + + + + + x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. + + UBERON:cjm + This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. + + conduit for + + + + + + + + + x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. + + GOC:cjm + + lumen of + + + + + + + + + s is luminal space of x iff s is lumen_of x and s is an immaterial entity + + + luminal space of + + + + + + + + A relation that holds between an attribute or a qualifier and another attribute. + + + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. + + has modifier + + + + + + + + + + + participates in a biotic-biotic interaction with + + + + + + + + + + inverse of has skeleton + + + skeleton of + + + + + + + + + + p directly regulates q iff p is immediately causally upstream of q and p regulates q. + + + directly regulates (processual) + + + + + directly regulates + + + + + + + + + holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y). + existence starts at end of + + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + + has part structure that is capable of + + + + + + + + + + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. + results in closure of + + + + + + + + + p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p + results in breakdown of + + + + + + + + + results in synthesis of + + + + + + + + + + + + + results in assembly of + + + + + + + + + p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. + results in catabolism of + + + + + + + + + + results in disassembly of + + + + + + + + + + results in remodeling of + + + + + + + + + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c + results in organization of + + + + + + + + + holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y). + existence ends at start of + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + + pazopanib -> pathological angiogenesis + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. + treats + + The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. + capable of inhibiting or preventing pathological process + + + + + treats + Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + + + + + + + + + benzene -> cancer [CHEBI] + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. + causes disease + + capable of upregulating or causing pathological process + + + + + + + + + c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. + treats + + is substance that treats + + + + + + + + + + c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. + May be ceded to OBI + is marker for + + + + + + + + + Inverse of 'causal agent in process' + + process has causal agent + + + + + + + + A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + obsolete related via dependence to + true + + + + + + + + A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Groups both positive and negative correlation + correlated with + + + + + + + + + An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. + A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. + In the Gene Ontology association model, this corresponds to the With/From field + is evidence with support from + + + + + + + + + Inverse of is-model-of + has model + + + + + + + + Do not use this relation directly. It is a grouping relation. + related via evidence or inference to + + + + + + + + + + visits + https://github.com/oborel/obo-relations/issues/74 + + + + + + + + + visited by + + + + + + + + + + visits flowers of + + + + + + + + + has flowers visited by + + + + + + + + + + + lays eggs in + + + + + + + + + + has eggs laid in by + + + + + + + + + + https://github.com/jhpoelen/eol-globi-data/issues/143 + kills + + + + + + + + + is killed by + + + + + + + + + + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. + + directly positively regulates (process to process) + + + + + directly positively regulates + + + + + + + + + + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. + + directly negatively regulates (process to process) + + + + + directly negatively regulates + + + + + + + + + + A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host + + ectoparasite of + + + + + + + + + inverse of ectoparasite of + + has ectoparasite + + + + + + + + + + + A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system + lives inside of + endoparasite of + + + + + + + + + has endoparasite + + + + + + + + + + A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite + mesoparasite of + + + + + + + + + inverse of mesoparasite of + + has mesoparasite + + + + + + + + + + A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. + + intercellular endoparasite of + + + + + + + + + inverse of intercellular endoparasite of + + has intercellular endoparasite + + + + + + + + + + A sub-relation of endoparasite-of in which the parasite inhabits host cells. + + intracellular endoparasite of + + + + + + + + + inverse of intracellular endoparasite of + + has intracellular endoparasite + + + + + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + + co-roosts with + + + + + + + + + + + + + + + + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + + + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + produces + + + + + + + + + a produced_by b iff some process that occurs_in b has_output a. + + + produced by + + + + + + + + + Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. + + represses expression of + + + + + + + + + Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. + + increases expression of + + + + + + + + + + A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + + is used to study + The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. + has role in modeling + + + + + + + + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + causes or contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. + causes condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. + contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. + contributes to expressivity of condition + contributes to severity of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. + contributes to penetrance of condition + contributes to frequency of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. + is preventative for condition + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + ameliorates condition + + + + + + + + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + + + + + + + + + A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. + exacerbates condition + + + + + + + + + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. + condition ameliorated by + + + + + + + + + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. + condition exacerbated by + + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a more specific relations + + 2017-11-05T02:38:20Z + condition has genetic basis in + + + + + + + + + + + 2017-11-05T02:45:20Z + has material basis in gain of function germline mutation in + + + + + + + + + + + + + 2017-11-05T02:45:37Z + has material basis in loss of function germline mutation in + + + + + + + + + + + 2017-11-05T02:45:54Z + has material basis in germline mutation in + + + + + + + + + + + + 2017-11-05T02:46:07Z + has material basis in somatic mutation in + + + + + + + + + + + + 2017-11-05T02:46:26Z + has major susceptibility factor + + + + + + + + + + + 2017-11-05T02:46:57Z + has partial material basis in germline mutation in + + + + + + + + + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. + + 2018-12-13T11:26:17Z + + has primary input or output + + + + + + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + + 2018-12-13T11:26:32Z + + has primary output + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + + 2018-12-13T11:26:56Z + + has primary input + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a more specific relations + + 2017-11-05T02:53:08Z + is genetic basis for condition + + + + + + + + + Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:55:51Z + is causal gain of function germline mutation of in + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:56:06Z + is causal loss of function germline mutation of in + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:56:40Z + is causal germline mutation in + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:57:07Z + is causal somatic mutation in + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. + + 2017-11-05T02:57:43Z + is causal susceptibility factor for + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. + + 2017-11-05T02:58:43Z + is causal germline mutation partially giving rise to + + + + + + + + + + + + 2017-11-05T03:20:01Z + realizable has basis in + + + + + + + + + + 2017-11-05T03:20:29Z + is basis for realizable + + + + + + + + + + + 2017-11-05T03:26:47Z + disease has basis in + + + + + + + + + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) + + 2017-11-05T03:29:32Z + disease has basis in dysfunction of + + + + + + + + + A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) + + 2017-11-05T03:37:52Z + disease has basis in disruption of + + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. + + 2017-11-05T03:46:07Z + disease has basis in feature + + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. + + 2017-11-05T03:50:54Z + causal relationship with disease as subject + + + + + + + + + + + + + + + + + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) + + 2017-11-05T03:51:09Z + disease causes disruption of + + + + + + + + + + + + + disease causes dysfunction of (disease to anatomical entity) + + 2017-11-05T03:58:20Z + disease causes dysfunction of + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. + TODO: complete range axiom once more of CARO has been mireoted in to this ontology + This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. + + 2017-11-05T04:06:02Z + disease has location + + + + + + + + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity + + 2017-12-26T19:37:31Z + disease has inflammation site + + + + + + + + + + + + + A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. + + 2017-12-26T19:45:49Z + realized in response to stimulus + + + + + + + + + A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. + + 2017-12-26T19:50:53Z + disease has feature + + + + + + + + + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. + + 2017-12-26T19:58:44Z + disease arises from alteration in structure + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + + 2018-01-25T23:20:13Z + enables subfunction + + + + + + + + + + + + + + + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. + DEPRECATED inheres in + true + + + + + + + + DEPRECATED bearer of + true + + + + + + + + A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity. + + has driver + + + + + + + + + + A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes. + + has disease driver + + + + + + + + + + + An interaction relationship wherein a plant or algae is living on the outside surface of another plant. + https://en.wikipedia.org/wiki/Epiphyte + epiphyte of + + + + + + + + + inverse of epiphyte of + + has epiphyte + + + + + + + + + + A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material + https://en.wikipedia.org/wiki/Kleptoparasitism + kleptoparasite of + + + + + + + + + inverse of kleptoparasite of + + kleptoparasitized by + + + + + + + + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. + creates habitat for + + + + + + + + + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. + ecologically co-occurs with + + + + + + + + + + An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. + lays eggs on + + + + + + + + + inverse of lays eggs on + has eggs laid on by + + + + + + + + + muffin 'has substance added' some 'baking soda' + + "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. + The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. + + has substance added + + + + + + + + + 'egg white' 'has substance removed' some 'egg yolk' + + "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. + + has substance removed + + + + + + + + + sardines 'immersed in' some 'oil and mustard' + + "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + + immersed in + + + + + + + + sardine has consumer some homo sapiens + + 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. + + has consumer + + + + + + + + + + bread 'has primary substance added' some 'flour' + + 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. + + has primary substance added + + + + + + + + + + + + + A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. + An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) + Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. + r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. + + + + + triggered by process + realized in response to + https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit + + + + + triggered by process + RO:cjm + + + + + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + + regulates activity of + + + + + + + + + The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. + + regulates quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. + + indirectly regulates activity of + + + + + + + + + The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. + +For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. + + decreases by repression quantity of + + + + + + + + + The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. + +For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. + + increases by expression quantity of + + + + + + + + + The entity A has an activity that directly positively regulates the quantity of B. + + directly positively regulates quantity of + + + + + + + + + The entity A has an activity that directly negatively regulates the quantity of B. + + directly negatively regulates quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. + + indirectly activates + indirectly positively regulates activity of + + + + + + + + + AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) + An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. + + destabilizes quantity of + + + + + + + + + AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) + An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. + + stabilizes quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. + + indirectly inhibits + indirectly negatively regulates activity of + + + + + + + + + The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. + + directly regulates quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. + + indirectly regulates quantity of + + + + + + + + + The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. + + indirectly negatively regulates quantity of + + + + + + + + + The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. + + indirectly positively regulates quantity of + + + + + + + + + + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg + 2020-04-22T20:27:26Z + has small molecule regulator + + + + + + + + + + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg + 2020-04-22T20:28:37Z + has small molecule activator + + + + + + + + + + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg + 2020-04-22T20:28:54Z + has small molecule inhibitor + + + + + + + + + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg + 2020-06-08T17:21:33Z + + + + acts on population of + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg + 2020-06-24T13:15:17Z + is small molecule regulator of + + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg + 2020-06-24T13:15:26Z + is small molecule activator of + + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg + 2020-06-24T13:15:35Z + is small molecule inhibitor of + + + + + + + + + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg + 2020-08-27T08:13:59Z + results in adhesion of + + + + + + + + + pg + 2021-02-26T07:28:29Z + + + + results in fusion of + + + + + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + + + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + + + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. + + 2020-07-17T09:26:52Z + has synaptic input or output in + has synaptic IO in region + + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. + + 2020-07-17T09:42:23Z + receives synaptic input in region + + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. + + 2020-07-17T09:45:06Z + sends synaptic output to region + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:52:19Z + has synaptic IO throughout + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:55:36Z + receives synaptic input throughout + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:57:27Z + sends synaptic output throughout + + + + + + + + + + + + + Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. + + 2020-07-20T12:10:09Z + has sensory dendrite location + has sensory terminal in + has sensory terminal location + has sensory dendrite in + + + + + + + + + + A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. + + 2021-05-26T08:40:18Z + receives synaptic input from neuron + + + + + + + + + A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. + + 2021-05-26T08:41:07Z + Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. + sends synaptic output to cell + + + + + + + + + A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. + + disease has infectious agent + + + + + + + + + + + + + transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) + A relation between a material entity and some data in which the data is taken as exemplifying the material entity. + C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. + + This relation is not meant to capture the relation between occurrents and data. + has exemplar data + + + + + + + + + exemplar data of + + + + + + + + + + A relation between a group and another group it is part of but does not fully constitute. + X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. + + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. + subcluster of + + + + + + + + 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1'). + transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3. + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + + + + + q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + different in magnitude relative to + + + + + q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + increased in magnitude relative to + + + + + q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + decreased in magnitude relative to + + + + + q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + similar in magnitude relative to + + + + + q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + has relative magnitude + + + + + + + + s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. + Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. + has cross section + + + + + s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + reciprocal of + + + + + q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') + A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. + + + has high plasma membrane amount + + + + + A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. + PMID:19243617 + + + + + + + + + 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') + A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. + + + has low plasma membrane amount + + + + + A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. + PMID:19243617 + + + + + + + + Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. + + 2021-11-05T17:30:14Z + has phenotype or disease + https://github.com/oborel/obo-relations/issues/478 + + + + + + + + + A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. + + 2021-11-05T17:30:44Z + has disease + https://github.com/oborel/obo-relations/issues/478 + + + + + + + + + X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. + ExO:0000083 + 2021-12-14T20:41:45Z + + has exposure medium + + + + + + + + + + + + A diagnostic testing device utilizes a specimen. + X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. + + + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08T12:00:00Z + utilizes + device utilizes material + + + + + + + + + Helper relation for OWL definition of RO:0018002 myristoylates + + is myristoyltransferase activity + + + + + + + + + + + + + + + A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input + + + myristoylates + + + + + + + + inverse of myristoylates + + myristoylated by + + + + + + + + + mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor + + is agonist of + + + + + + + + + + pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level + + is inverse agonist of + + + + + + + + + + tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level + + is antagonist of + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + negatively regulates characteristic + + + + + + + + + Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. + + confers susceptibility to condition + + + + + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + + 2018-09-26T00:00:32Z + disease relationship + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + + 2018-09-26T01:08:58Z + results in changes to anatomical or cellular structure + + + + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + TODO: Add homeomorphy axiom + + + + + ECO:0000041 + SO:similar_to + sameness + similar to + correspondence + resemblance + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + + + + + + + + + + + + Similarity that results from common evolutionary origin. + + + homologous to + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + + + + + + + + + + + + + Similarity that results from independent evolution. + + + homoplasous to + analogy + in homoplasy relationship with + + + + + + Similarity that results from independent evolution. + + + + + + + + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + ECO:0000075 + homocracous to + Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + in homocracy relationship with + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + + + + + + + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + analogy + Convergence usually implies a notion of adaptation. + in convergence relationship with + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + + + + + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + parallel evolution + Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + in parallelism relationship with + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + + + + + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + ECO:0000071 + MI:2163 + structural homologous to + idealistic homology + in structural homology relationship with + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by common descent. + + + homology + ECO:0000080 + RO_proposed_relation:homologous_to + SO:0000330 + SO:0000853 + SO:0000857 + SO:homologous_to + TAO:homologous_to + cladistic homology + historical homologous to + phylogenetic homology + taxic homology + true homology + in historical homology relationship with + + + + + + Homology that is defined by common descent. + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + ECO:0000067 + biological homologous to + transformational homology + Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + in biological homology relationship with + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + + + + + + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + atavism + rudiment + reversion + in reversal relationship with + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + + + + + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + + MeSH:Synteny + SO:0000860 + SO:0005858 + syntenic homologous to + synteny + in syntenic homology relationship with + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + MeSH:Synteny + + + + + + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + SO:0000854 + SO:0000859 + SO:paralogous_to + paralogous to + in paralogy relationship with + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + + + + + + + + + + + + + Paralogy that involves sets of syntenic blocks. + + + syntenic paralogous to + duplicon + paralogon + in syntenic paralogy relationship with + + + + + + Paralogy that involves sets of syntenic blocks. + + + DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y + + + + + + + + + + Syntenic homology that involves chromosomes of different species. + + + syntenic orthologous to + in syntenic orthology relationship with + + + + + + Syntenic homology that involves chromosomes of different species. + + + + + + + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + + fractional homology + partial homologous to + segmental homology + mixed homology + modular homology + partial correspondence + percent homology + in partial homology relationship with + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + ISBN:0123195837 + ISBN:978-0471984931 + + + + + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + MeSH:Structural_Homology,_Protein + protein structural homologous to + in protein structural homology relationship with + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + + + + + + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + + pseudogene + SO:non_functional_homolog_of + non functional homologous to + in non functional homology relationship with + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + SO:non_functional_homolog_of + + + + + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + ECO:00000060 + SO:0000855 + SO:0000858 + SO:orthologous_to + orthologous to + The term is sometimes also used for anatomical structures. + in orthology relationship with + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + + + + + + + + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + xenologous to + The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + in xenology relationship with + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + + + + + + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + + 1 to 1 homologous to + 1:1 homology + one-to-one homology + in 1 to 1 homology relationship with + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + BGEE:curator + + + + + + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + 1 to 1 orthologous to + 1:1 orthology + one-to-one orthology + in 1 to 1 orthology relationship with + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + + + + + + + + + + + Paralogy that results from a whole genome duplication event. + + + ohnologous to + homoeology + in ohnology relationship with + + + + + + Paralogy that results from a whole genome duplication event. + + + + + + + + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + in-paralogous to + inparalogy + symparalogy + in in-paralogy relationship with + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + + + + + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + alloparalogy + out-paralogous to + outparalogy + in out-paralogy relationship with + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + + + + + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + pro-orthologous to + in pro-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + + + + + + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + semi-orthologous to + The converse of pro-orthologous. + in semi-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + + + + + + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + serial homologous to + homonomy + in serial homology relationship with + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + + + + + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + + heterochronous homologous to + heterochrony + in heterochronous homology relationship with + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + ISBN:978-0674639416 + + + + + + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + juvenification + pedomorphosis + in paedomorphorsis relationship with + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + ISBN:978-0674639416 + + + + + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + in peramorphosis relationship with + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + + + + + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + in progenesis relationship with + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + ISBN:978-0674639416 + + + + + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + juvenilization + neotenous to + in neoteny relationship with + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + ISBN:978-0674639416 + + + + + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + mimicrous to + in mimicry relationship with + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + + + + + + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + 1 to many orthologous to + 1:many orthology + one-to-many orthology + co-orthology + many to 1 orthology + in 1 to many orthology relationship with + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + + + + + + + + + + + Historical homology that involves two members of a larger set of homologs. + + + many to many homologous to + many-to-many homology + many:many homology + in many to many homology relationship with + + + + + + Historical homology that involves two members of a larger set of homologs. + + + + + + + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + + 1 to many homologous to + one-to-many homology + 1:many homology + in 1 to many homology relationship with + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + BGEE:curator + + + + + + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + + apomorphous to + synapomorphy + in apomorphy relationship with + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + ISBN:978-0252068140 + + + + + + + + + + Historical homology that is based on distant shared ancestry. + + + plesiomorphous to + symplesiomorphy + This term is usually contrasted to apomorphy. + in plesiomorphy relationship with + + + + + + Historical homology that is based on distant shared ancestry. + + ISBN:978-0252068140 + + + + + + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + deep genetic homology + deep homologous to + generative homology + homoiology + Used for structures in distantly related taxa. + in deep homology relationship with + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + + + + + + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + hemiplasous to + in hemiplasy relationship with + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + + + + + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + gametologous to + in gametology relationship with + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + + + + + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + + MeSH:Chromosome_Pairing + chromosomal homologous to + in chromosomal homology relationship with + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + ISBN:0195307615 + + + + + + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + many to many orthologous to + many-to-many orthology + many:many orthology + trans-orthology + co-orthology + trans-homology + in many to many orthology relationship with + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + + + + + + + + + + + + Paralogy that involves genes from the same species. + + + within-species paralogous to + in within-species paralogy relationship with + + + + + + Paralogy that involves genes from the same species. + + + + + + + + + + + + Paralogy that involves genes from different species. + + + between-species paralogous to + The genes have diverged before a speciation event. + in between-species paralogy relationship with + + + + + + Paralogy that involves genes from different species. + + + + + + + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + post-displacement + in postdisplacement relationship with + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + + + + + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + in hypermorphosis relationship with + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + ISBN:978-0674639416 + + + + + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + synologous to + in synology relationship with + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + + + + + + + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + ECO:0000080 + isoorthologous to + in isoorthology relationship with + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + tandem paralogous to + iterative paralogy + serial paralogy + in tandem paralogy relationship with + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + ISBN:978-0878932665 + + + + + + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + apomorphic tendency + cryptic homology + latent homologous to + underlying synapomorphy + homoiology + homoplastic tendency + re-awakening + Used for structures in closely related taxa. + in latent homology relationship with + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + + + ISBN:0199141118 + + + + + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + generative homology + syngenous to + Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + in syngeny relationship with + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R + + + + + + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + 1:1 paralogy + apparent 1:1 orthology + apparent orthologous to + pseudoorthology + The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + in apparent orthology relationship with + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + + + + + + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + pseudoparalogous to + These genes may come out as paralogs in a single-genome analysis. + in pseudoparalogy relationship with + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + + + + + + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + equivalogous to + This may include examples of orthology, paralogy and xenology. + in equivalogy relationship with + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + interologous to + in interology relationship with + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + + + + + + + + + + + Similarity that is characterized by interchangeability in function. + + + functional similarity + in functional equivalence relationship with + + + + + + Similarity that is characterized by interchangeability in function. + + + + + + + + + + + + + Biological homology that involves parts of the same organism. + + + iterative homologous to + in iterative homology relationship with + + + + + + Biological homology that involves parts of the same organism. + + + + + + + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + duplicate xenology + multiple xenology + paraxenologous to + in paraxenology relationship with + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + + + + + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + plerologous to + This phenomenon is usually due to gene conversion process. + in plerology relationship with + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + + + + + + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + homotopous to + Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + in homotopy relationship with + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + + ISBN:0123195837 + + + + + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + heterotopy + in homeosis relationship with + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + + + + + + + + + + + + Synology that results from allopolyploidy. + + + homoeologous to + On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + in homoeology relationship with + + + + + + Synology that results from allopolyploidy. + + + + + + + + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + axis paramorphism + in paramorphism relationship with + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + + + + + + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + regulogous to + in regulogy relationship with + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + + + + + + + + + + + + + + + + + + 0 + + + 100 + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + dos + 2018-05-22T16:43:28Z + This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. + has increased age-specific mortality rate + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + PMID:24138933 + Wikipedia:Infant_mortality + + + + + + + + + + + + + ## Elucidation + +This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + +## How to interpret (informal) + +First the &quot;atemporal&quot; FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + axiom holds for all times + + + + + + + + ## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y) + relation has no temporal argument + + + + + + + + + curation status specification + + + + ready for release + + + + pending final vetting + + + + obsolescence reason specification + + + + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-chado.tsv b/src/ontology/subsets/ro-chado.tsv new file mode 100644 index 00000000..e69de29b diff --git a/src/ontology/subsets/ro-developmental.json b/src/ontology/subsets/ro-developmental.json new file mode 100644 index 00000000..4c466e7e --- /dev/null +++ b/src/ontology/subsets/ro-developmental.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-developmental.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_2D_boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_2D_boundary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "lbl" : "electrically_synapsed_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions." + }, + "xrefs" : [ { + "val" : "RO:0002003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "electrically_synapsed_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002007" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "lbl" : "coincident with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." + }, + "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002008" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note from NCEAS meeting: consider changing primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "coincident_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "lbl" : "regulates in other organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "xrefs" : [ { + "val" : "RO:0002010" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_in_other_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "lbl" : "occurrent part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A part of relation that applies only between occurrents." + }, + "xrefs" : [ { + "val" : "RO:0002012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurrent_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." + }, + "xrefs" : [ { + "val" : "RO:0002013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "xrefs" : [ { + "val" : "RO:0002014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_negative_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], + "xrefs" : [ { + "val" : "RO:0002015" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_positive_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "lbl" : "has necessary component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], + "xrefs" : [ { + "val" : "RO:0002016" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_necessary_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], + "xrefs" : [ { + "val" : "RO:0002017" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:44:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "xrefs" : [ { + "val" : "RO:0002018" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "lbl" : "has ligand", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." + }, + "xrefs" : [ { + "val" : "RO:0002019" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-19T17:30:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ligand" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "lbl" : "transports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." + }, + "xrefs" : [ { + "val" : "RO:0002020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:11:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." + }, + "xrefs" : [ { + "val" : "RO:0002021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "xrefs" : [ { + "val" : "RO:0002022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:38Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. 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No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." + }, + "xrefs" : [ { + "val" : "RO:0002104" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : 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"synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002106" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that 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it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002113" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "synapses in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_presynaptic_terminal_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002114", + "lbl" : "synapsed_via_type_III_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." + }, + "comments" : [ "Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002114" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_via_type_III_bouton_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002115", + "lbl" 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 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}, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002297" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002298" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_morphogenesis_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_maturation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002300" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_disappearance_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002301" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_regression_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002302" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_treated_by_substance" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002303" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_habitat" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002304" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002305" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002309" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stimulus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002313" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports_or_maintains_localization_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "xrefs" : [ { + "val" : "RO:0002314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : 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"http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_acquisition_of_features_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002321" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "colocalizes_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002326" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002327" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enables" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "xrefs" : [ { + "val" : "RO:0002328" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "functionally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "xrefs" : [ { + "val" : "RO:0002329" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_structure_that_is_capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "xrefs" : [ { + "val" : "RO:0002331" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "xrefs" : [ { + "val" : "RO:0002332" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_levels_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002333" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enabled_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002334" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002335" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002336" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "xrefs" : [ { + "val" : "RO:0002337" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_localization_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002338" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002339" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002340" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "imports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "xrefs" : [ { + "val" : "RO:0002341" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_along" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002342" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002343" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_growth_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002344" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' 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"http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "exports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002348", + "lbl" : "results in commitment to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002348" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. 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It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. 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"RO:0002445" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitized_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. 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We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "subject_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002463" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "target_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002469" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_nutrients_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002470" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "eats" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002471" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_eaten_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002473" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "composed_primarily_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "xrefs" : [ { + "val" : "RO:0002476" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/subsets/ro-developmental.obo b/src/ontology/subsets/ro-developmental.obo index 0d29373a..f8e39bda 100644 --- a/src/ontology/subsets/ro-developmental.obo +++ b/src/ontology/subsets/ro-developmental.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-developmental -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/src/ontology/subsets/ro-developmental.owl b/src/ontology/subsets/ro-developmental.owl index 27c2e134..a7ea63b4 100644 --- a/src/ontology/subsets/ro-developmental.owl +++ b/src/ontology/subsets/ro-developmental.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-developmental.tsv b/src/ontology/subsets/ro-developmental.tsv new file mode 100644 index 00000000..42281381 --- /dev/null +++ b/src/ontology/subsets/ro-developmental.tsv @@ -0,0 +1,51 @@ +?x ?label +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid1 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid18 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid22 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid26 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid33 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid37 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid40 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid5 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid52 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid58 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid61 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid64 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid67 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-eco.json b/src/ontology/subsets/ro-eco.json new file mode 100644 index 00000000..ad70b049 --- /dev/null +++ b/src/ontology/subsets/ro-eco.json @@ -0,0 +1,13048 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-eco.owl", + "meta" : { + "version" : "http://purl.obolibrary.org/obo/ro/http://purl.obolibrary.org/obo/ro-edit.owl/subsets/ro-eco.owl" + }, + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", 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"OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons." + }, + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000301", + "lbl" : "obsolete upstream in neural circuit with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first." + }, + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000302", + "lbl" : "obsolete downstream in neural circuit with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first." + }, + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001018", + "lbl" : "contained in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "contained in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001019", + "lbl" : "contains", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "contains" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001900", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002001", + "lbl" : "aligned with", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "lbl" : "electrically_synapsed_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002004", + "lbl" : "tracheates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002005", + "lbl" : "innervated_by", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "lbl" : "coincident with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." + }, + "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note from NCEAS meeting: consider changing primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002009", + "lbl" : "cell expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "lbl" : "regulates in other organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002011", + "lbl" : "regulates transport of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a process that regulates a transport process and the entity transported by that process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "lbl" : "occurrent part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A part of relation that applies only between occurrents." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "lbl" : "has necessary component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:44:33Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "lbl" : "has ligand", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-19T17:30:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "lbl" : "transports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:11:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:38Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002029", + "lbl" : "has increased age-specific mortality rate", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.", + "xrefs" : [ "PMID:24138933", "Wikipedia:Infant_mortality" ] + }, + "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T16:43:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "di" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002105", + "lbl" : "synapsed_via_type_Ib_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton." + }, + "comments" : [ "Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002106", + "lbl" : "synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002107", + "lbl" : "synapsed_via_type_II_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." + }, + "comments" : [ "Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002108", + "lbl" : "synapsed_by_via_type_II_bouton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type II bouton." + }, + "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002109", + "lbl" : "synapsed_by_via_type_Ib_bouton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton." + }, + "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : 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some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002115", + "lbl" : "synapsed_by_via_type_III_bouton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type III bouton.\n" + }, + "comments" : [ "Expands to: has_part some ('presynaptic membrane' 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"http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "lbl" : "derived by descent from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral_stucture_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "evolutionarily_descended_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "lbl" : "has derived by descendant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of derived by descent from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "lbl" : "serially homologous to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + }, + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9227-417X" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002171", + "lbl" : "mutually spatially disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "non-overlapping with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no parts with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX owl: \nPREFIX part_of: \nPREFIX mutually_spatially_disjoint_with: \nCONSTRUCT {\n part_of: a owl:ObjectProperty .\n [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?x ;\n owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?y\n ]\n ]\n}\nWHERE {\n ?x mutually_spatially_disjoint_with: ?y .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/RO_0002163" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002172", + "lbl" : "taxonomic class assertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002173", + "lbl" : "ambiguous for taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002174", + "lbl" : "dubious for taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T." + }, + "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" + }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002204", + "lbl" : "gene product of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "lbl" : "has gene product", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002214", + "lbl" : "has prototype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002217", + "lbl" : "obsolete actively participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" + }, + "comments" : [ "Obsoleted as the inverse property was obsoleted." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "agent in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002608" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002218", + "lbl" : "obsolete has active participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has agent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002500" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002245", + "lbl" : "over-expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002246", + "lbl" : "under-expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "lbl" : "defined by inverse", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002291", + "lbl" : "ubiquitously expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'expressed in'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002293", + "lbl" : "ubiquitously expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ubiquiotously expressed in" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002312", + "lbl" : "evolutionary variant of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" + }, { + "pred" : 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changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002349", + "lbl" : "results in determination of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "lbl" : "input of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has input" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "lbl" : "output of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has output" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "lbl" : "formed as result of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002355", + "lbl" : "results in structural organization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002356", + "lbl" : "results in specification of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002374", + "lbl" : "derived from ancestral fusion of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" + }, + "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "has fused element" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002401", + "lbl" : "obsolete has indirect input", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002402", + "lbl" : "obsolete has direct output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "translation SubClassOf has_direct_output some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly produces" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002403", + "lbl" : "obsolete has indirect output", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002406", + "lbl" : "obsolete directly activates", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002629" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002408", + "lbl" : "obsolete directly inhibits", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002630" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002416", + "lbl" : "logical macro assertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002419", + "lbl" : "annotation property cardinality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002420", + "lbl" : "logical macro assertion on a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a class" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002421", + "lbl" : "logical macro assertion on a property", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a property" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002422", + "lbl" : "logical macro assertion on an object property", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "lbl" : "logical macro assertion on an annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002424", + "lbl" : "differs in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This is an exploratory relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002425", + "lbl" : "differs in attribute of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "lbl" : "differs in attribute", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000316" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0208" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "lbl" : "molecularly interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "binds" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "molecularly binds with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0915" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002437", + "lbl" : "biotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "interacts with on organism level" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/interactsWith" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002438", + "lbl" : "trophically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the partners are related via a feeding relationship." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "lbl" : "preys on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Baleen whale preys on krill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7134-3324" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of predation interaction with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preys upon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/preysUpon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.inaturalist.org/observations/2942824" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002440", + "lbl" : "symbiotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction in which the two organisms live together in more or less intimate association." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002441", + "lbl" : "commensually interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002442", + "lbl" : "mutualistically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "lbl" : "interacts with via parasite-host interaction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002444", + "lbl" : "parasite of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "direct parasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Pediculus humanus capitis parasite of human" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitizes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/parasitizes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002445", + "lbl" : "parasitized by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "directly parasitized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "semibiotically interacts with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Porifiera attaches to substrate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002447", + "lbl" : "phosphorylates", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "lbl" : "directly regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly decreases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly inhibits" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "lbl" : "directly positively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly increases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly activates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002451", + "lbl" : "transmitted by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a disease and organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "all dengue disease transmitted by some mosquito" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Add domain and range constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002452", + "lbl" : "has symptom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between a disease or an organism and a phenotype" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002453", + "lbl" : "host of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "lbl" : "has host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasHost" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002455", + "lbl" : "pollinates", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Bees pollinate Flowers" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/pollinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "lbl" : "pollinated by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has polinator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasPollinator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "lbl" : "acquires nutrients from", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002458", + "lbl" : "preyed upon by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of preys on" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has predator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of predation interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/HasPredator" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "lbl" : "is vector for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002460", + "lbl" : "has vector", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002461", + "lbl" : "partner in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002462", + "lbl" : "subject participant in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002464", + "lbl" : "helper property (not for use in curation)", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002465", + "lbl" : "is symbiosis", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002466", + "lbl" : "is commensalism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002467", + "lbl" : "is mutualism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002468", + "lbl" : "is parasitism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002472", + "lbl" : "is evidence for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002474", + "lbl" : "dispositional interpretation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002475", + "lbl" : "has no connections with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no connection with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002481", + "lbl" : "is kinase activity", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002482", + "lbl" : "is ubiquitination", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002483", + "lbl" : "inherited annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002484", + "lbl" : "curator guidance link", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "exists during" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/BFO_0000169" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002503", + "lbl" : "towards", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002504", + "lbl" : "always present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brain always_present_in_taxon 'Vertebrata'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "forelimb always_present_in_taxon Euarchontoglires" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "never lost in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002505", + "lbl" : "has intermediate", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has intermediate product" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002506", + "lbl" : "causal relation between entities", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002507", + "lbl" : "determined by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A coral reef environment is determined by a particular coral reef" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/24330602" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determined by (system to material entity)" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002508", + "lbl" : "determines", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of determined by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determines (material entity to system)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002509", + "lbl" : "determined by part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002510", + "lbl" : "transcribed from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is transcribed from y if and only if x is synthesized from template y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002511", + "lbl" : "transcribed to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of transcribed from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002512", + "lbl" : "ribosomal translation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002513", + "lbl" : "ribosomally translates to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ribosomal translation of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002514", + "lbl" : "sequentially related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are sequentially adjacent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002516", + "lbl" : "has start sequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002518", + "lbl" : "has end sequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ended by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002519", + "lbl" : "is end sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has end sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002520", + "lbl" : "is consecutive sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the SO paper, this was defined as an instance-type relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002521", + "lbl" : "is sequentially aligned with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "lbl" : "bounds sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002523", + "lbl" : "is bound by sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of bounds sequence of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "lbl" : "has subsequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contains" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "lbl" : "is subsequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has subsequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained by" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "lbl" : "overlaps sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002527", + "lbl" : "does not overlap sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "disconnected from" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "lbl" : "is upstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of downstream of sequence of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "lbl" : "is downstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002530", + "lbl" : "is immediately downstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002529" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002531", + "lbl" : "is immediately upstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of immediately downstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002535", + "lbl" : "temporal logical macro assertion on a class", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002536", + "lbl" : "measurement property has unit", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002537", + "lbl" : "has start time value", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002538", + "lbl" : "has end time value", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002539", + "lbl" : "start, days post fertilization", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002540", + "lbl" : "end, days post fertilization", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002541", + "lbl" : "start, years post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002542", + "lbl" : "end, years post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002543", + "lbl" : "start, months post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002544", + "lbl" : "end, months post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002545", + "lbl" : "month of gestation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002546", + "lbl" : "has developmental stage marker", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002547", + "lbl" : "start, days post coitum", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of coitum." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002548", + "lbl" : "end, days post coitum", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the end of the stage and the time of coitum." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002549", + "lbl" : "start, weeks post birth", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002550", + "lbl" : "end, weeks post birth", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002551", + "lbl" : "has skeleton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has supporting framework" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002552", + "lbl" : "results in ending of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002553", + "lbl" : "hyperparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "hyperparasitoid of" + }, { + "pred" : "hasRelatedSynonym", + "val" : "epiparasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://eol.org/schema/terms/hyperparasitoidOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Hyperparasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "lbl" : "hyperparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of hyperparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "has epiparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has hyperparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hyperparasitoidized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002555", + "lbl" : "allelopath of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Allelopathy" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/allelopathyYes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002556", + "lbl" : "pathogen of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002557", + "lbl" : "has pathogen", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002558", + "lbl" : "has evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of is evidence for" + }, + "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/25052702" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "lbl" : "causally influenced by", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influenced by (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002560", + "lbl" : "is asymmetric relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002561", + "lbl" : "is symmetric relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002562", + "lbl" : "is relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "lbl" : "interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "lbl" : "molecular interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002565", + "lbl" : "results in movement of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "lbl" : "causally influences", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "lbl" : "biomechanically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002568", + "lbl" : "has muscle antagonist", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Antagonist_(muscle)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002569", + "lbl" : "has branching part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of branching part of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "lbl" : "conduit for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "UBERON:cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002571", + "lbl" : "lumen of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:cjm" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002572", + "lbl" : "luminal space of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002573", + "lbl" : "has modifier", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between an attribute or a qualifier and another attribute." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002574", + "lbl" : "participates in a biotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002575", + "lbl" : "is direct form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002423", + "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "lbl" : "skeleton of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has skeleton" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "lbl" : "directly regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002579", + "lbl" : "is indirect form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002580", + "lbl" : "logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002581", + "lbl" : "is a defining property chain axiom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002583", + "lbl" : "existence starts at end of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002584", + "lbl" : "has part structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002585", + "lbl" : "results in closure of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002586", + "lbl" : "results in breakdown of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002587", + "lbl" : "results in synthesis of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002588", + "lbl" : "results in assembly of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002589", + "lbl" : "results in catabolism of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002590", + "lbl" : "results in disassembly of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002591", + "lbl" : "results in remodeling of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002592", + "lbl" : "results in organization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002593", + "lbl" : "existence ends at start of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002594", + "lbl" : "is relational form of a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "lbl" : "causal relation between material entity and a process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002596", + "lbl" : "capable of regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pyrethroid -> growth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "lbl" : "capable of negatively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "lbl" : "capable of positively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "renin -> arteriolar smooth muscle contraction" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002599", + "lbl" : "capable of inhibiting or preventing pathological process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pazopanib -> pathological angiogenesis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002600", + "lbl" : "capable of upregulating or causing pathological process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "benzene -> cancer [CHEBI]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "causes disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002601", + "lbl" : "logical macro assertion involving identity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A shortcut relationship that holds between two entities based on their identity criteria" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002602", + "lbl" : "in approximate one to one relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002603", + "lbl" : "is approximately equivalent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002604", + "lbl" : "is opposite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002605", + "lbl" : "is indistinguishable from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002606", + "lbl" : "is substance that treats", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002607", + "lbl" : "is marker for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be ceded to OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002608", + "lbl" : "process has causal agent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'causal agent in process'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002609", + "lbl" : "obsolete related via dependence to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002610", + "lbl" : "correlated with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Groups both positive and negative correlation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002611", + "lbl" : "evidential logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002612", + "lbl" : "axiom has evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002613", + "lbl" : "axiom contradicted by evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002614", + "lbl" : "is evidence with support from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." + }, + "comments" : [ "In the Gene Ontology association model, this corresponds to the With/From field" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002615", + "lbl" : "has model", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of is-model-of" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002616", + "lbl" : "related via evidence or inference to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002617", + "lbl" : "is representative IRI for equivalence set", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002618", + "lbl" : "visits", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/74" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002619", + "lbl" : "visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002622", + "lbl" : "visits flowers of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002623", + "lbl" : "has flowers visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002624", + "lbl" : "lays eggs in", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002625", + "lbl" : "has eggs laid in by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002626", + "lbl" : "kills", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://github.com/jhpoelen/eol-globi-data/issues/143" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002627", + "lbl" : "is killed by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "lbl" : "directly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002630", + "lbl" : "directly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002632", + "lbl" : "ectoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002633", + "lbl" : "has ectoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ectoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002634", + "lbl" : "endoparasite of", + "type" : "PROPERTY", + "meta" : { + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "lives inside of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002635", + "lbl" : "has endoparasite", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002636", + "lbl" : "mesoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002637", + "lbl" : "has mesoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of mesoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002638", + "lbl" : "intercellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002639", + "lbl" : "has intercellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intercellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002640", + "lbl" : "intracellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002641", + "lbl" : "has intracellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intracellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002801", + "lbl" : "co-roosts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Communal_roosting" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003000", + "lbl" : "produces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." + }, + "comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "lbl" : "produced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a produced_by b iff some process that occurs_in b has_output a." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003002", + "lbl" : "represses expression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003003", + "lbl" : "increases expression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "lbl" : "has role in modeling", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." + }, + "comments" : [ "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-1048-5019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is used to study" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "lbl" : "causes or contributes to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." + }, + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003303", + "lbl" : "causes condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "lbl" : "contributes to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "lbl" : "contributes to severity of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to expressivity of condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003306", + "lbl" : "contributes to frequency of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to penetrance of condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "lbl" : "ameliorates condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." + }, + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preventative for condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003308", + "lbl" : "correlated with condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003309", + "lbl" : "exacerbates condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003310", + "lbl" : "condition ameliorated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003311", + "lbl" : "condition exacerbated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004000", + "lbl" : "condition has genetic basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:38:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004001", + "lbl" : "has material basis in gain of function germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:20Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410295" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410296" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004002", + "lbl" : "has material basis in loss of function germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004003", + "lbl" : "has material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:54Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004004", + "lbl" : "has material basis in somatic mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:07Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004005", + "lbl" : "has major susceptibility factor", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:26Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004006", + "lbl" : "has partial material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:57Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004007", + "lbl" : "has primary input or output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004008", + "lbl" : "has primary output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", + "xrefs" : [ "GOC:kva", "GOC:pt", "GOC:cjm", "GOC:dph" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004009", + "lbl" : "has primary input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", + "xrefs" : [ "GOC:kva", "GOC:pt", "GOC:cjm", "GOC:dph" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:56Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004010", + "lbl" : "is genetic basis for condition", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:53:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004011", + "lbl" : "is causal gain of function germline mutation of in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : 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"http://purl.obolibrary.org/obo/RO_0004013", + "lbl" : "is causal germline mutation in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:56:40Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004014", + "lbl" : "is causal somatic mutation in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:57:07Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004015", + "lbl" : "is causal susceptibility factor for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + 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"http://purl.obolibrary.org/obo/RO_0004017", + "lbl" : "realizable has basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:01Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004018", + "lbl" : "is basis for realizable", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004019", + "lbl" : "disease has basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:26:47Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004020", + "lbl" : "disease has basis in dysfunction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in dysfunction of (disease to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:29:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004021", + "lbl" : "disease has basis in disruption of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:37:52Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004022", + "lbl" : "disease has basis in feature", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the 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It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:50:54Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004024", + "lbl" : "disease causes disruption of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:51:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004025", + "lbl" : "disease causes dysfunction of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes dysfunction of (disease to anatomical entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:58:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004026", + "lbl" : "disease has location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T04:06:02Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004027", + "lbl" : "disease has inflammation site", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:37:31Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004029", + "lbl" : "disease has feature", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:50:53Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "lbl" : "disease arises from alteration in structure", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "lbl" : "enables subfunction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-25T23:20:13Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "lbl" : "acts upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:30Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "lbl" : "acts upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:51Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "lbl" : "acts upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "lbl" : "acts upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004036", + "lbl" : "nominally disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004048", + "lbl" : "is directional form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:59:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004049", + "lbl" : "is positive form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:16Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007000", + "lbl" : "has driver", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007001", + "lbl" : "has disease driver", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008501", + "lbl" : "epiphyte of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Epiphyte" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008502", + "lbl" : "has epiphyte", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of epiphyte of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008503", + "lbl" : "kleptoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008504", + "lbl" : "kleptoparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of kleptoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008505", + "lbl" : "creates habitat for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008506", + "lbl" : "ecologically co-occurs with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008507", + "lbl" : "lays eggs on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008508", + "lbl" : "has eggs laid on by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of lays eggs on" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009001", + "lbl" : "has substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "muffin 'has substance added' some 'baking soda'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009002", + "lbl" : "has substance removed", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'egg white' 'has substance removed' some 'egg yolk'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009003", + "lbl" : "immersed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardines 'immersed in' some 'oil and mustard'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009004", + "lbl" : "has consumer", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardine has consumer some homo sapiens" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009005", + "lbl" : "has primary substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bread 'has primary substance added' some 'flour'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "lbl" : "realized in response to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "triggered by process", + "xrefs" : [ "RO:cjm" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : 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"receives synaptic input throughout", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:55:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013006", + "lbl" : "sends synaptic output throughout", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:57:27Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013007", + "lbl" : "has sensory dendrite in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has sensory dendrite location" + }, { + "pred" : "hasExactSynonym", + "val" : "has sensory terminal in" + }, { + "pred" : "hasExactSynonym", + "val" : "has sensory terminal location" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-20T12:10:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013008", + "lbl" : "receives synaptic input from neuron", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-05-26T08:40:18Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013009", + "lbl" : "sends synaptic output to cell", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." + }, + "comments" : [ "Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-05-26T08:41:07Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0014001", + "lbl" : "disease has infectious agent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015001", + "lbl" : "has exemplar data", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-5260-9315" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is not meant to capture the relation between occurrents and data." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015002", + "lbl" : "exemplar data of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-5260-9315" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015003", + "lbl" : "subcluster of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a group and another group it is part of but does not fully constitute." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7258-9596" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context." + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015006", + "lbl" : "different in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015007", + "lbl" : "increased in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "lbl" : "decreased in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015009", + "lbl" : "similar in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "lbl" : "has relative magnitude", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015011", + "lbl" : "has cross section", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015012", + "lbl" : "reciprocal of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015015", + "lbl" : "has high plasma membrane amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "lbl" : "has low plasma membrane amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016001", + "lbl" : "has phenotype or disease", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016002", + "lbl" : "has disease", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:44Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016004", + "lbl" : "has exposure medium", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000083" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-12-14T20:41:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7463-6306" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017001", + "lbl" : "device utilizes material", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "utilizes" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A diagnostic testing device utilizes a specimen." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-2620-0345" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-11-08T12:00:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018001", + "lbl" : "is myristoyltransferase activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Helper relation for OWL definition of RO:0018002 myristoylates" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018002", + "lbl" : "myristoylates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/conformsTo", + "val" : "http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018003", + "lbl" : "myristoylated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of myristoylates" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018027", + "lbl" : "is agonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P3772" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018028", + "lbl" : "is inverse agonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + 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"http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002380", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002377", "http://purl.obolibrary.org/obo/RO_0002381" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002413", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002402", "http://purl.obolibrary.org/obo/RO_0002400" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002409" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002403", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002402" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002553", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002444", "http://purl.obolibrary.org/obo/RO_0002444" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002554", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002445", "http://purl.obolibrary.org/obo/RO_0002445" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000062" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/RO_0002082" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000063" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002509", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002507", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002205", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002511", "http://purl.obolibrary.org/obo/RO_0002513" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002204", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002512", "http://purl.obolibrary.org/obo/RO_0002510" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002526", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002524", "http://purl.obolibrary.org/obo/RO_0002525" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002583", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002593", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004024", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013002", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013003", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013003", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013007", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0015001", "http://purl.obolibrary.org/obo/RO_0015003" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/subsets/ro-eco.obo b/src/ontology/subsets/ro-eco.obo index 7f3fab39..1bf9637b 100644 --- a/src/ontology/subsets/ro-eco.obo +++ b/src/ontology/subsets/ro-eco.obo @@ -7,7 +7,6 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: ro/subsets/ro-eco -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: BFO:0000050 @@ -177,7 +176,7 @@ is_a: RO:0001018 ! contained in [Typedef] id: RO:0002005 name: innervated_by -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI +property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 inverse_of: RO:0002134 ! innervates @@ -685,7 +684,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -788,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -798,8 +797,8 @@ name: connected to def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -809,8 +808,8 @@ def: "c connects a if and only if there exist some b such that a and b are simil property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -1120,7 +1119,7 @@ is_a: RO:0002220 ! adjacent to [Typedef] id: RO:0002222 subset: ro-eco -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string @@ -1259,28 +1258,28 @@ property_value: IAO:0000232 "This object property is needed for axioms using has id: RO:0002240 name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002241 name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: RO:0002309 ! has exposure stimulus [Typedef] id: RO:0002242 name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002243 name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: RO:0002244 ! related via exposure to [Typedef] @@ -1370,7 +1369,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string is_a: RO:0002258 ! developmentally preceded by @@ -1492,7 +1491,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1506,7 +1505,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -1522,7 +1521,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1537,7 +1536,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1654,7 +1653,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1967,7 +1966,7 @@ is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps @@ -1987,7 +1986,7 @@ id: RO:0002372 name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -1997,7 +1996,7 @@ id: RO:0002373 name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -2024,7 +2023,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -2039,11 +2038,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with @@ -2058,7 +2057,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with @@ -2090,7 +2089,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 holds_over_chain: RO:0002377 RO:0002381 is_a: BFO:0000050 @@ -2337,7 +2336,7 @@ name: differs in comment: This is an exploratory relation property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions xsd:anyURI +property_value: seeAlso "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" xsd:anyURI [Typedef] id: RO:0002425 @@ -2427,18 +2426,18 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_symmetric: true [Typedef] id: RO:0002435 name: genetically interacts with -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 @@ -2449,7 +2448,7 @@ is_a: RO:0002434 ! interacts with id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -2465,7 +2464,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string is_symmetric: true is_a: RO:0002321 ! ecologically related to is_a: RO:0002434 ! interacts with @@ -2491,8 +2490,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002458 ! preyed upon by @@ -2502,7 +2501,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -2513,7 +2512,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -2522,7 +2521,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -2531,7 +2530,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -2543,7 +2542,7 @@ synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002454 ! has host inverse_of: RO:0002445 ! parasitized by @@ -2556,7 +2555,7 @@ synonym: "directly parasitized by" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002453 ! host of @@ -2639,7 +2638,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -2650,7 +2649,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: RO:0002442 ! mutualistically interacts with inverse_of: RO:0002456 ! pollinated by @@ -2661,7 +2660,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: RO:0002442 ! mutualistically interacts with [Typedef] @@ -2682,8 +2681,8 @@ subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: RO:0002438 ! trophically interacts with [Typedef] @@ -3058,7 +3057,7 @@ id: RO:0002510 name: transcribed from def: "x is transcribed from y if and only if x is synthesized from template y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002511 ! transcribed to @@ -3068,7 +3067,7 @@ name: transcribed to def: "inverse of transcribed from" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to [Typedef] @@ -3076,7 +3075,7 @@ id: RO:0002512 name: ribosomal translation of def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002513 ! ribosomally translates to @@ -3085,7 +3084,7 @@ id: RO:0002513 name: ribosomally translates to def: "inverse of ribosomal translation of" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to [Typedef] @@ -3094,7 +3093,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -3107,7 +3106,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002527 ! does not overlap sequence of [Typedef] @@ -3118,7 +3117,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002524 ! has subsequence inverse_of: RO:0002517 ! is start sequence of @@ -3131,7 +3130,7 @@ subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002525 ! is subsequence of @@ -3143,7 +3142,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002524 ! has subsequence inverse_of: RO:0002519 ! is end sequence of @@ -3156,7 +3155,7 @@ subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002525 ! is subsequence of @@ -3167,7 +3166,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002524 ! has subsequence [Typedef] @@ -3208,7 +3207,7 @@ def: "x has subsequence y iff all of the sequence parts of y are sequence parts property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: BFO:0000051 is_a: RO:0002522 ! bounds sequence of @@ -3318,8 +3317,8 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string holds_over_chain: RO:0002444 RO:0002444 is_a: RO:0002454 ! has host inverse_of: RO:0002554 ! hyperparasitized by @@ -3342,8 +3341,8 @@ id: RO:0002555 name: allelopath of subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -3387,7 +3386,7 @@ id: RO:0002563 name: interaction relation helper property property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] @@ -3430,7 +3429,7 @@ id: RO:0002568 name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: RO:0002567 ! biomechanically related to [Typedef] @@ -3450,7 +3449,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string is_a: RO:0002131 ! overlaps @@ -3460,7 +3459,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string is_a: BFO:0000050 [Typedef] @@ -3695,7 +3694,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping [Typedef] id: RO:0002618 name: visits -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002619 ! visited by @@ -3731,7 +3730,7 @@ is_a: RO:0002619 ! visited by [Typedef] id: RO:0002626 name: kills -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002627 ! is killed by @@ -3770,7 +3769,7 @@ is_a: RO:0002578 ! directly regulates id: RO:0002632 name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002444 ! parasite of inverse_of: RO:0002633 ! has ectoparasite @@ -3786,7 +3785,7 @@ id: RO:0002634 name: endoparasite of synonym: "lives inside of" RELATED [] property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002444 ! parasite of inverse_of: RO:0002635 ! has endoparasite @@ -3813,7 +3812,7 @@ is_a: RO:0002445 ! parasitized by id: RO:0002638 name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002639 ! has intercellular endoparasite @@ -3828,7 +3827,7 @@ is_a: RO:0002635 ! has endoparasite id: RO:0002640 name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002641 ! has intracellular endoparasite @@ -4322,7 +4321,7 @@ is_a: RO:0007000 ! has driver id: RO:0008501 name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: RO:0002440 ! symbiotically interacts with inverse_of: RO:0008502 ! has epiphyte @@ -4337,7 +4336,7 @@ is_a: RO:0002440 ! symbiotically interacts with id: RO:0008503 name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: RO:0002444 ! parasite of inverse_of: RO:0008504 ! kleptoparasitized by @@ -4428,7 +4427,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI is_a: RO:0002410 ! causally related to [Typedef] @@ -4872,25 +4871,25 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0016001 name: has phenotype or disease property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease [Typedef] id: RO:0016004 name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: RO:0002244 ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 diff --git a/src/ontology/subsets/ro-eco.tsv b/src/ontology/subsets/ro-eco.tsv new file mode 100644 index 00000000..e69de29b diff --git a/src/ontology/subsets/ro-hom.json b/src/ontology/subsets/ro-hom.json new file mode 100644 index 00000000..ade7fe10 --- /dev/null +++ b/src/ontology/subsets/ro-hom.json @@ -0,0 +1,2808 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-hom.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "lbl" : "derived by descent from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." + }, + "xrefs" : [ { + "val" : "RO:0002156" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral_stucture_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "evolutionarily_descended_from" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "derived_by_descent_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "lbl" : "has derived by descendant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of derived by descent from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002157" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_derived_by_descendant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ], + "xrefs" : [ { + "val" : "RO:0002158" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "shares_ancestor_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "lbl" : "serially homologous to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002159" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "serially_homologous_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." + }, + "xrefs" : [ { + "val" : "RO:0002160" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "only_in_taxon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + }, + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002162" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9227-417X" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_taxon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002312", + "lbl" : "evolutionary variant of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002312" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "evolutionary_variant_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process" + }, + "xrefs" : [ { + "val" : "RO:0002320" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "evolutionarily_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002374", + "lbl" : "derived from ancestral fusion of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" + }, + "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "has fused element" + } ], + "xrefs" : [ { + "val" : "RO:0002374" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "derived_from_ancestral_fusion_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "lbl" : "in similarity relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000000", "BGEE:curator" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "sameness" + }, { + "pred" : "hasExactSynonym", + "val" : "similar to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "correspondence", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "resemblance" + } ], + "xrefs" : [ { + "val" : "ECO:0000041" + }, { + "val" : "SO:similar_to" + }, { + "val" : "RO:HOM0000000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_similarity_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000000" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000001", + "lbl" : "in homology relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Similarity that results from common evolutionary origin.", + "xrefs" : [ "http://dx.doi.org/10.1002/bies.950180611", "http://dx.doi.org/10.1002/jmor.1051730307", "http://dx.doi.org/10.1007/BF02814480", "http://purl.obolibrary.org/obo/HOM_0000001" ] + }, + "comments" : [ "This broad definition encompasses all the working definitions proposed so far in the literature." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homologous to" + } ], + "xrefs" : [ { + "val" : "RO:HOM0000001" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_homology_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000001" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000002", + "lbl" : "in homoplasy relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Similarity that results from independent evolution.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000002" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homoplasous to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "analogy" + } ], + "xrefs" : [ { + "val" : "RO:HOM0000002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_homoplasy_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000002" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000003", + "lbl" : "in homocracy relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814484", "http://dx.doi.org/10.1007/s00427-003-0301-4", "http://dx.doi.org/10.1186/1742-9994-2-15", "http://purl.obolibrary.org/obo/HOM_0000003" ] + }, + "comments" : [ "Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homocracous to" + } ], + "xrefs" : [ { + "val" : "ECO:0000075" + }, { + "val" : "RO:HOM0000003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_homocracy_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000003" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000004", + "lbl" : "in convergence relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Homoplasy that involves different underlying mechanisms or structures.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000004" ] + }, + "comments" : [ "Convergence usually implies a notion of adaptation." ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "analogy" + } ], + "xrefs" : [ { + "val" : "RO:HOM0000004" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_convergence_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000004" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000005", + "lbl" : "in parallelism relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Homoplasy that involves homologous underlying mechanisms or structures.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000005" ] + }, + "comments" : [ "Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "parallel evolution" + } ], + "xrefs" : [ { + "val" : "RO:HOM0000005" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_parallelism_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000006", + "lbl" : "in structural homology relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Homology that is defined by similarity with regard to selected structural parameters.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.014", "http://dx.doi.org/10.1146/annurev.es.20.110189.000411", "http://purl.obolibrary.org/obo/HOM_0000006", "ISBN:0123195837" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "structural homologous to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "idealistic homology" + } ], + "xrefs" : [ { + "val" : "ECO:0000071" + }, { + "val" : "MI:2163" + }, { + "val" : "RO:HOM0000006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_structural_homology_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000006" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000007", + "lbl" : "in historical homology relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Homology that is defined by common descent.", + "xrefs" : [ "http://dx.doi.org/10.1016/S0169-5347(97)01125-7", "http://purl.obolibrary.org/obo/HOM_0000007", "ISBN:0123195837" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "homology" + }, { + "pred" : "hasExactSynonym", + "val" : "cladistic homology" + }, { + "pred" : "hasExactSynonym", + "val" : "historical homologous to" + }, { + "pred" : "hasExactSynonym", + "val" : "phylogenetic homology" + }, { + "pred" : "hasExactSynonym", + "val" : "taxic homology" + }, { + "pred" : "hasRelatedSynonym", + 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"http://purl.obolibrary.org/obo/RO_HOM0000043", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000044", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000044", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000005" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000045", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000046", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000047" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000047", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000048", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000048", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000036" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000049", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000050", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000051", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000029" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000052", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000053", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000018" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000054", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000054", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000062" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000055", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000057", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000005" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000057", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000058" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000058", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000060", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000019" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000060", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000050" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000061", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000018" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000062", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000062", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000065" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000063", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000065", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000066", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000008" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000068", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000018" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000069", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000071", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000006" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000072", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000008" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000073", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000073", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000053" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000074", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000074", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000066" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000075", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002156", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002157" + } ], + "domainRangeAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/subsets/ro-hom.obo b/src/ontology/subsets/ro-hom.obo index 301fb31e..27d2a0be 100644 --- a/src/ontology/subsets/ro-hom.obo +++ b/src/ontology/subsets/ro-hom.obo @@ -1,10 +1,1018 @@ format-version: 1.2 ontology: ro/subsets/ro-hom +[Typedef] +id: derived_by_descent_from +name: derived by descent from +def: "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." [] +xref: RO:0002156 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "ancestral_stucture_of" xsd:string +property_value: IAO:0000118 "evolutionarily_descended_from" xsd:string +is_transitive: true +is_a: evolutionarily_related_to ! evolutionarily related to +inverse_of: has_derived_by_descendant ! has derived by descendant + +[Typedef] +id: derived_from_ancestral_fusion_of +name: derived from ancestral fusion of +def: "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" [] +comment: A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. +synonym: "has fused element" BROAD [] +xref: RO:0002374 +property_value: IAO:0000112 "false" xsd:boolean +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 +is_a: derived_by_descent_from ! derived by descent from + +[Typedef] +id: evolutionarily_related_to +name: evolutionarily related to +def: "A relationship that holds via some environmental process" [] +xref: RO:0002320 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string + +[Typedef] +id: evolutionary_variant_of +name: evolutionary variant of +xref: RO:0002312 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: evolutionarily_related_to ! evolutionarily related to + +[Typedef] +id: has_derived_by_descendant +name: has derived by descendant +def: "inverse of derived by descent from" [] +subset: RO:0002259 +xref: RO:0002157 +property_value: IAO:0000114 IAO:0000125 +is_transitive: true +is_a: evolutionarily_related_to ! evolutionarily related to + +[Typedef] +id: in_1_to_1_homology_relationship_with +name: in 1 to 1 homology relationship with +def: "Historical homology that involves two members sharing no other homologs in the lineages considered." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000019] +synonym: "1 to 1 homologous to" EXACT [] +synonym: "1:1 homology" EXACT [] +synonym: "one-to-one homology" EXACT [] +xref: RO:HOM0000019 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000019 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_1_to_1_orthology_relationship_with +name: in 1 to 1 orthology relationship with +def: "Orthology that involves two genes that did not experience any duplication after the speciation event that created them." [http://dx.doi.org/10.1007/BF02814484, http://purl.obolibrary.org/obo/HOM_0000020, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "1 to 1 orthologous to" EXACT [] +synonym: "1:1 orthology" EXACT [] +synonym: "one-to-one orthology" EXACT [] +xref: RO:HOM0000020 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000020 +is_symmetric: true +is_a: in_1_to_1_homology_relationship_with ! in 1 to 1 homology relationship with +is_a: in_orthology_relationship_with ! in orthology relationship with + +[Typedef] +id: in_1_to_many_homology_relationship_with +name: in 1 to many homology relationship with +def: "Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000037] +synonym: "1 to many homologous to" EXACT [] +synonym: "1:many homology" RELATED [] +synonym: "one-to-many homology" EXACT [] +xref: RO:HOM0000037 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000037 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_1_to_many_orthology_relationship_with +name: in 1 to many orthology relationship with +def: "Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000034, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "1 to many orthologous to" EXACT [] +synonym: "1:many orthology" EXACT [] +synonym: "co-orthology" RELATED [] +synonym: "many to 1 orthology" RELATED [] +synonym: "one-to-many orthology" EXACT [] +xref: RO:HOM0000034 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000034 +is_symmetric: true +is_a: in_1_to_many_homology_relationship_with ! in 1 to many homology relationship with +is_a: in_orthology_relationship_with ! in orthology relationship with + +[Typedef] +id: in_apomorphy_relationship_with +name: in apomorphy relationship with +def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [http://purl.obolibrary.org/obo/HOM_0000042, ISBN:978-0252068140] +synonym: "apomorphous to" EXACT [] +synonym: "synapomorphy" RELATED [] +xref: RO:HOM0000042 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000042 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with +disjoint_from: in_plesiomorphy_relationship_with ! in plesiomorphy relationship with + +[Typedef] +id: in_apparent_orthology_relationship_with +name: in apparent orthology relationship with +def: "Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000060, http://www.ensembl.org/info/docs/compara/homology_method.html] +comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. +synonym: "1:1 paralogy" EXACT [] +synonym: "apparent 1:1 orthology" EXACT [] +synonym: "apparent orthologous to" EXACT [] +synonym: "pseudoorthology" EXACT [] +xref: RO:HOM0000060 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000060 +is_symmetric: true +is_a: in_1_to_1_homology_relationship_with ! in 1 to 1 homology relationship with +is_a: in_between-species_paralogy_relationship_with ! in between-species paralogy relationship with + +[Typedef] +id: in_between-species_paralogy_relationship_with +name: in between-species paralogy relationship with +def: "Paralogy that involves genes from different species." [http://purl.obolibrary.org/obo/HOM_0000050, http://www.ensembl.org/info/docs/compara/homology_method.html] +comment: The genes have diverged before a speciation event. +synonym: "between-species paralogous to" EXACT [] +xref: RO:HOM0000050 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000050 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with + +[Typedef] +id: in_biological_homology_relationship_with +name: in biological homology relationship with +def: "Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000008] +comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. +synonym: "biological homologous to" EXACT [] +synonym: "transformational homology" RELATED [] +xref: ECO:0000067 +xref: RO:HOM0000008 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000008 +is_symmetric: true +is_a: in_homology_relationship_with ! in homology relationship with + +[Typedef] +id: in_chromosomal_homology_relationship_with +name: in chromosomal homology relationship with +def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [http://purl.obolibrary.org/obo/HOM_0000047, ISBN:0195307615] +synonym: "chromosomal homologous to" EXACT [] +xref: MeSH:Chromosome_Pairing +xref: RO:HOM0000047 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000047 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_convergence_relationship_with +name: in convergence relationship with +def: "Homoplasy that involves different underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000004] +comment: Convergence usually implies a notion of adaptation. +synonym: "analogy" RELATED [] +xref: RO:HOM0000004 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000004 +is_symmetric: true +is_a: in_homoplasy_relationship_with ! in homoplasy relationship with + +[Typedef] +id: in_deep_homology_relationship_with +name: in deep homology relationship with +def: "Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1038/nature07891, http://purl.obolibrary.org/obo/HOM_0000044] +comment: Used for structures in distantly related taxa. +synonym: "deep genetic homology" EXACT [] +synonym: "deep homologous to" EXACT [] +synonym: "generative homology" RELATED [] +synonym: "homoiology" RELATED [] +xref: RO:HOM0000044 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000044 +is_symmetric: true +is_a: in_homocracy_relationship_with ! in homocracy relationship with +is_a: in_parallelism_relationship_with ! in parallelism relationship with + +[Typedef] +id: in_equivalogy_relationship_with +name: in equivalogy relationship with +def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1093/nar/gkl1043, http://purl.obolibrary.org/obo/HOM_0000062] +comment: This may include examples of orthology, paralogy and xenology. +synonym: "equivalogous to" EXACT [] +xref: RO:HOM0000062 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000062 +is_symmetric: true +is_a: in_functional_equivalence_relationship_with ! in functional equivalence relationship with +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_functional_equivalence_relationship_with +name: in functional equivalence relationship with +def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] +synonym: "functional similarity" RELATED [] +xref: RO:HOM0000065 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000065 +is_symmetric: true +is_a: in_similarity_relationship_with ! in similarity relationship with + +[Typedef] +id: in_gametology_relationship_with +name: in gametology relationship with +def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] +synonym: "gametologous to" EXACT [] +xref: RO:HOM0000046 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000046 +is_symmetric: true +is_a: in_chromosomal_homology_relationship_with ! in chromosomal homology relationship with + +[Typedef] +id: in_hemiplasy_relationship_with +name: in hemiplasy relationship with +def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] +synonym: "hemiplasous to" EXACT [] +xref: RO:HOM0000045 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000045 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_heterochronous_homology_relationship_with +name: in heterochronous homology relationship with +def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [http://purl.obolibrary.org/obo/HOM_0000028, ISBN:978-0674639416] +synonym: "heterochronous homologous to" EXACT [] +synonym: "heterochrony" EXACT [] +xref: RO:HOM0000028 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000028 +is_symmetric: true +is_a: in_biological_homology_relationship_with ! in biological homology relationship with + +[Typedef] +id: in_historical_homology_relationship_with +name: in historical homology relationship with +def: "Homology that is defined by common descent." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://purl.obolibrary.org/obo/HOM_0000007, ISBN:0123195837] +synonym: "cladistic homology" EXACT [] +synonym: "historical homologous to" EXACT [] +synonym: "homology" BROAD [] +synonym: "phylogenetic homology" EXACT [] +synonym: "taxic homology" EXACT [] +synonym: "true homology" RELATED [] +xref: ECO:0000080 +xref: RO:HOM0000007 +xref: RO_proposed_relation:homologous_to +xref: SO:0000330 +xref: SO:0000853 +xref: SO:0000857 +xref: SO:homologous_to +xref: TAO:homologous_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000007 +is_symmetric: true +is_a: in_homology_relationship_with ! in homology relationship with + +[Typedef] +id: in_homeosis_relationship_with +name: in homeosis relationship with +def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] +synonym: "heterotopy" RELATED [] +xref: RO:HOM0000072 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000072 +is_symmetric: true +is_a: in_biological_homology_relationship_with ! in biological homology relationship with + +[Typedef] +id: in_homocracy_relationship_with +name: in homocracy relationship with +def: "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/s00427-003-0301-4, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000003] +comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. +synonym: "homocracous to" EXACT [] +xref: ECO:0000075 +xref: RO:HOM0000003 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000003 +is_symmetric: true +is_a: evolutionarily_related_to ! evolutionarily related to +is_a: in_similarity_relationship_with ! in similarity relationship with + +[Typedef] +id: in_homoeology_relationship_with +name: in homoeology relationship with +def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pnas.0505156102, http://purl.obolibrary.org/obo/HOM_0000073] +comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. +synonym: "homoeologous to" EXACT [] +xref: RO:HOM0000073 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000073 +is_symmetric: true +is_a: in_ohnology_relationship_with ! in ohnology relationship with +is_a: in_synology_relationship_with ! in synology relationship with + +[Typedef] +id: in_homology_relationship_with +name: in homology relationship with +def: "Similarity that results from common evolutionary origin." [http://dx.doi.org/10.1002/bies.950180611, http://dx.doi.org/10.1002/jmor.1051730307, http://dx.doi.org/10.1007/BF02814480, http://purl.obolibrary.org/obo/HOM_0000001] +comment: This broad definition encompasses all the working definitions proposed so far in the literature. +synonym: "homologous to" EXACT [] +xref: RO:HOM0000001 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000001 +is_symmetric: true +is_a: in_similarity_relationship_with ! in similarity relationship with +is_a: shares_ancestor_with ! shares ancestor with +disjoint_from: in_homoplasy_relationship_with ! in homoplasy relationship with + +[Typedef] +id: in_homoplasy_relationship_with +name: in homoplasy relationship with +def: "Similarity that results from independent evolution." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000002] +synonym: "analogy" RELATED [] +synonym: "homoplasous to" EXACT [] +xref: RO:HOM0000002 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000002 +is_symmetric: true +is_a: in_similarity_relationship_with ! in similarity relationship with + +[Typedef] +id: in_homotopy_relationship_with +name: in homotopy relationship with +def: "Structural homology that involves structures with the same or similar relative positions." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/BF02814485, http://purl.obolibrary.org/obo/HOM_0000071, ISBN:0123195837] +comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. +synonym: "homotopous to" EXACT [] +xref: RO:HOM0000071 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000071 +is_symmetric: true +is_a: in_structural_homology_relationship_with ! in structural homology relationship with +disjoint_from: in_homeosis_relationship_with ! in homeosis relationship with + +[Typedef] +id: in_hypermorphosis_relationship_with +name: in hypermorphosis relationship with +def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] +xref: RO:HOM0000052 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000052 +is_symmetric: true +is_a: in_peramorphosis_relationship_with ! in peramorphosis relationship with + +[Typedef] +id: in_in-paralogy_relationship_with +name: in in-paralogy relationship with +def: "Paralogy that results from a lineage-specific duplication subsequent to a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000023] +synonym: "in-paralogous to" EXACT [] +synonym: "inparalogy" EXACT [] +synonym: "symparalogy" EXACT [] +xref: RO:HOM0000023 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000023 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with +disjoint_from: in_out-paralogy_relationship_with ! in out-paralogy relationship with + +[Typedef] +id: in_interology_relationship_with +name: in interology relationship with +def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] +synonym: "interologous to" EXACT [] +xref: RO:HOM0000063 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000063 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_isoorthology_relationship_with +name: in isoorthology relationship with +def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000054] +synonym: "isoorthologous to" EXACT [] +xref: ECO:0000080 +xref: RO:HOM0000054 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000054 +is_symmetric: true +is_a: in_equivalogy_relationship_with ! in equivalogy relationship with +is_a: in_orthology_relationship_with ! in orthology relationship with + +[Typedef] +id: in_iterative_homology_relationship_with +name: in iterative homology relationship with +def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] +synonym: "iterative homologous to" EXACT [] +xref: RO:HOM0000066 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000066 +is_symmetric: true +is_a: in_biological_homology_relationship_with ! in biological homology relationship with + +[Typedef] +id: in_latent_homology_relationship_with +name: in latent homology relationship with +def: "Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character)." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000057, ISBN:0199141118] +comment: Used for structures in closely related taxa. +synonym: "apomorphic tendency" EXACT [] +synonym: "cryptic homology" EXACT [] +synonym: "homoiology" RELATED [] +synonym: "homoplastic tendency" RELATED [] +synonym: "latent homologous to" EXACT [] +synonym: "re-awakening" RELATED [] +synonym: "underlying synapomorphy" EXACT [] +xref: RO:HOM0000057 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000057 +is_symmetric: true +is_a: in_parallelism_relationship_with ! in parallelism relationship with +is_a: in_syngeny_relationship_with ! in syngeny relationship with + +[Typedef] +id: in_many_to_many_homology_relationship_with +name: in many to many homology relationship with +def: "Historical homology that involves two members of a larger set of homologs." [http://dx.doi.org/10.1093/molbev/msp002, http://purl.obolibrary.org/obo/HOM_0000036] +synonym: "many to many homologous to" EXACT [] +synonym: "many-to-many homology" EXACT [] +synonym: "many:many homology " EXACT [] +xref: RO:HOM0000036 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000036 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_many_to_many_orthology_relationship_with +name: in many to many orthology relationship with +def: "Orthology that involves two genes that experienced duplications more recent than the species split that created them." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000048, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "co-orthology" RELATED [] +synonym: "many to many orthologous to" EXACT [] +synonym: "many-to-many orthology" EXACT [] +synonym: "many:many orthology" EXACT [] +synonym: "trans-homology" RELATED [] +synonym: "trans-orthology" EXACT [] +xref: RO:HOM0000048 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000048 +is_symmetric: true +is_a: in_many_to_many_homology_relationship_with ! in many to many homology relationship with +is_a: in_orthology_relationship_with ! in orthology relationship with + +[Typedef] +id: in_mimicry_relationship_with +name: in mimicry relationship with +def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033] +synonym: "mimicrous to" EXACT [] +xref: RO:HOM0000033 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000033 +is_symmetric: true +is_a: in_convergence_relationship_with ! in convergence relationship with + +[Typedef] +id: in_neoteny_relationship_with +name: in neoteny relationship with +def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, http://purl.obolibrary.org/obo/HOM_0000032, ISBN:978-0674639416] +synonym: "juvenilization" EXACT [] +synonym: "neotenous to" EXACT [] +xref: RO:HOM0000032 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000032 +is_symmetric: true +is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with + +[Typedef] +id: in_non_functional_homology_relationship_with +name: in non functional homology relationship with +def: "Structural homology that involves a pseudogenic feature and its functional ancestor." [http://purl.obolibrary.org/obo/HOM_0000016, SO:non_functional_homolog_of] +synonym: "non functional homologous to" EXACT [] +synonym: "pseudogene" BROAD [] +xref: RO:HOM0000016 +xref: SO:non_functional_homolog_of +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000016 +is_symmetric: true +is_a: in_structural_homology_relationship_with ! in structural homology relationship with +disjoint_from: in_equivalogy_relationship_with ! in equivalogy relationship with + +[Typedef] +id: in_ohnology_relationship_with +name: in ohnology relationship with +def: "Paralogy that results from a whole genome duplication event." [http://dx.doi.org/10.1038/75560, http://purl.obolibrary.org/obo/HOM_0000022] +synonym: "homoeology" RELATED [] +synonym: "ohnologous to" EXACT [] +xref: RO:HOM0000022 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000022 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with + +[Typedef] +id: in_orthology_relationship_with +name: in orthology relationship with +def: "Historical homology that involves genes that diverged after a speciation event." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000017, http://www.ncbi.nlm.nih.gov/pubmed/5449325] +comment: The term is sometimes also used for anatomical structures. +synonym: "orthologous to" EXACT [] +xref: ECO:00000060 +xref: RO:HOM0000017 +xref: SO:0000855 +xref: SO:0000858 +xref: SO:orthologous_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000017 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_out-paralogy_relationship_with +name: in out-paralogy relationship with +def: "Paralogy that results from a duplication preceding a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000024] +synonym: "alloparalogy" EXACT [] +synonym: "out-paralogous to" EXACT [] +synonym: "outparalogy" EXACT [] +xref: RO:HOM0000024 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000024 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with + +[Typedef] +id: in_paedomorphorsis_relationship_with +name: in paedomorphorsis relationship with +def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000029, ISBN:978-0674639416] +synonym: "juvenification" EXACT [] +synonym: "pedomorphosis" EXACT [] +xref: RO:HOM0000029 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000029 +is_symmetric: true +is_a: in_heterochronous_homology_relationship_with ! in heterochronous homology relationship with +disjoint_from: in_peramorphosis_relationship_with ! in peramorphosis relationship with + +[Typedef] +id: in_parallelism_relationship_with +name: in parallelism relationship with +def: "Homoplasy that involves homologous underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000005] +comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. +synonym: "parallel evolution" EXACT [] +xref: RO:HOM0000005 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000005 +is_symmetric: true +is_a: in_homoplasy_relationship_with ! in homoplasy relationship with + +[Typedef] +id: in_paralogy_relationship_with +name: in paralogy relationship with +def: "Historical homology that involves genes that diverged after a duplication event." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000011, http://www.ncbi.nlm.nih.gov/pubmed/5449325] +synonym: "paralogous to" EXACT [] +xref: RO:HOM0000011 +xref: SO:0000854 +xref: SO:0000859 +xref: SO:paralogous_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000011 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with +disjoint_from: in_orthology_relationship_with ! in orthology relationship with + +[Typedef] +id: in_paramorphism_relationship_with +name: in paramorphism relationship with +def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] +synonym: "axis paramorphism" RELATED [] +xref: RO:HOM0000074 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000074 +is_symmetric: true +is_a: in_homocracy_relationship_with ! in homocracy relationship with +is_a: in_iterative_homology_relationship_with ! in iterative homology relationship with + +[Typedef] +id: in_paraxenology_relationship_with +name: in paraxenology relationship with +def: "Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome." [http://purl.obolibrary.org/obo/HOM_0000068, http://www.ncbi.nlm.nih.gov/pubmed/3065587] +synonym: "duplicate xenology" EXACT [] +synonym: "multiple xenology" EXACT [] +synonym: "paraxenologous to" EXACT [] +xref: RO:HOM0000068 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000068 +is_symmetric: true +is_a: in_xenology_relationship_with ! in xenology relationship with + +[Typedef] +id: in_partial_homology_relationship_with +name: in partial homology relationship with +def: "Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous." [http://purl.obolibrary.org/obo/HOM_0000014, ISBN:0123195837, ISBN:978-0471984931] +synonym: "fractional homology" EXACT [] +synonym: "mixed homology" RELATED [] +synonym: "modular homology" RELATED [] +synonym: "partial correspondence" RELATED [] +synonym: "partial homologous to" EXACT [] +synonym: "percent homology" RELATED [] +synonym: "segmental homology" EXACT [] +xref: RO:HOM0000014 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000014 +is_symmetric: true +is_a: in_structural_homology_relationship_with ! in structural homology relationship with + +[Typedef] +id: in_peramorphosis_relationship_with +name: in peramorphosis relationship with +def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] +xref: RO:HOM0000030 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000030 +is_symmetric: true +is_a: in_heterochronous_homology_relationship_with ! in heterochronous homology relationship with + +[Typedef] +id: in_plerology_relationship_with +name: in plerology relationship with +def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [http://purl.obolibrary.org/obo/HOM_0000069, http://www.ncbi.nlm.nih.gov/pubmed/3065587] +comment: This phenomenon is usually due to gene conversion process. +synonym: "plerologous to" EXACT [] +xref: RO:HOM0000069 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000069 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with + +[Typedef] +id: in_plesiomorphy_relationship_with +name: in plesiomorphy relationship with +def: "Historical homology that is based on distant shared ancestry." [http://purl.obolibrary.org/obo/HOM_0000043, ISBN:978-0252068140] +comment: This term is usually contrasted to apomorphy. +synonym: "plesiomorphous to" EXACT [] +synonym: "symplesiomorphy" RELATED [] +xref: RO:HOM0000043 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000043 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_postdisplacement_relationship_with +name: in postdisplacement relationship with +def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] +synonym: "post-displacement" EXACT [] +xref: RO:HOM0000051 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000051 +is_symmetric: true +is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with + +[Typedef] +id: in_pro-orthology_relationship_with +name: in pro-orthology relationship with +def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] +synonym: "pro-orthologous to" EXACT [] +xref: RO:HOM0000025 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000025 +is_symmetric: true +is_a: in_1_to_many_orthology_relationship_with ! in 1 to many orthology relationship with + +[Typedef] +id: in_progenesis_relationship_with +name: in progenesis relationship with +def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] +xref: RO:HOM0000031 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000031 +is_symmetric: true +is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with + +[Typedef] +id: in_protein_structural_homology_relationship_with +name: in protein structural homology relationship with +def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [http://dx.doi.org/10.1016/0022-2836(76)90195-9, http://purl.obolibrary.org/obo/HOM_0000015] +synonym: "protein structural homologous to" EXACT [] +xref: MeSH:Structural_Homology\,_Protein +xref: RO:HOM0000015 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000015 +is_symmetric: true +is_a: in_structural_homology_relationship_with ! in structural homology relationship with + +[Typedef] +id: in_pseudoparalogy_relationship_with +name: in pseudoparalogy relationship with +def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000061] +comment: These genes may come out as paralogs in a single-genome analysis. +synonym: "pseudoparalogous to" EXACT [] +xref: RO:HOM0000061 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000061 +is_symmetric: true +is_a: in_xenology_relationship_with ! in xenology relationship with + +[Typedef] +id: in_regulogy_relationship_with +name: in regulogy relationship with +def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] +synonym: "regulogous to" EXACT [] +xref: RO:HOM0000075 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000075 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_reversal_relationship_with +name: in reversal relationship with +def: "Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000009] +synonym: "atavism" EXACT [] +synonym: "reversion" RELATED [] +synonym: "rudiment" EXACT [] +xref: RO:HOM0000009 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000009 +is_symmetric: true +is_a: in_homoplasy_relationship_with ! in homoplasy relationship with + +[Typedef] +id: in_semi-orthology_relationship_with +name: in semi-orthology relationship with +def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000026] +comment: The converse of pro-orthologous. +synonym: "semi-orthologous to" EXACT [] +xref: RO:HOM0000026 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000026 +is_symmetric: true +is_a: in_1_to_many_orthology_relationship_with ! in 1 to many orthology relationship with + +[Typedef] +id: in_serial_homology_relationship_with +name: in serial homology relationship with +def: "Iterative homology that involves structures arranged along the main body axis." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000027] +synonym: "homonomy" RELATED [] +synonym: "serial homologous to" EXACT [] +xref: RO:HOM0000027 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000027 +is_symmetric: true +is_a: in_iterative_homology_relationship_with ! in iterative homology relationship with + [Typedef] id: in_similarity_relationship_with +name: in similarity relationship with +def: "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000000] +synonym: "correspondence" RELATED [http://dx.doi.org/10.1007/BF02814479] +synonym: "resemblance" RELATED [] +synonym: "sameness" EXACT [] +synonym: "similar to" EXACT [] +xref: ECO:0000041 xref: RO:HOM0000000 +xref: SO:similar_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: IAO:0000116 "TODO: Add homeomorphy axiom" xsd:string property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 +property_value: seeAlso HOM:0000000 +is_symmetric: true + +[Typedef] +id: in_structural_homology_relationship_with +name: in structural homology relationship with +def: "Homology that is defined by similarity with regard to selected structural parameters." [http://dx.doi.org/10.1016/j.jhevol.2006.11.014, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000006, ISBN:0123195837] +synonym: "idealistic homology" RELATED [] +synonym: "structural homologous to" EXACT [] +xref: ECO:0000071 +xref: MI:2163 +xref: RO:HOM0000006 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000006 +is_symmetric: true +is_a: in_homology_relationship_with ! in homology relationship with + +[Typedef] +id: in_syngeny_relationship_with +name: in syngeny relationship with +def: "Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual." [DOI:10.1002/1521-1878(200009)22\:9<846\:\:AID-BIES10>3.0.CO;2-R, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000058] +comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. +synonym: "generative homology" EXACT [] +synonym: "syngenous to" EXACT [] +xref: RO:HOM0000058 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000058 +is_symmetric: true +is_a: in_homocracy_relationship_with ! in homocracy relationship with + +[Typedef] +id: in_synology_relationship_with +name: in synology relationship with +def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] +synonym: "synologous to" EXACT [] +xref: RO:HOM0000053 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000053 +is_symmetric: true +is_a: in_xenology_relationship_with ! in xenology relationship with + +[Typedef] +id: in_syntenic_homology_relationship_with +name: in syntenic homology relationship with +def: "Structural homology that is detected by similarity in content and organization between chromosomes." [http://purl.obolibrary.org/obo/HOM_0000010, MeSH:Synteny] +synonym: "syntenic homologous to" EXACT [] +synonym: "synteny" RELATED [] +xref: MeSH:Synteny +xref: RO:HOM0000010 +xref: SO:0000860 +xref: SO:0005858 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000010 +is_symmetric: true +is_a: in_structural_homology_relationship_with ! in structural homology relationship with + +[Typedef] +id: in_syntenic_orthology_relationship_with +name: in syntenic orthology relationship with +def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] +synonym: "syntenic orthologous to" EXACT [] +xref: RO:HOM0000013 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000013 +is_symmetric: true +is_a: in_syntenic_homology_relationship_with ! in syntenic homology relationship with + +[Typedef] +id: in_syntenic_paralogy_relationship_with +name: in syntenic paralogy relationship with +def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20001215)288\:4<345\:\:AID-JEZ7>3.0.CO;2-Y, http://dx.doi.org/10.1186/1471-213X-7-100, http://purl.obolibrary.org/obo/HOM_0000012] +synonym: "duplicon" RELATED [] +synonym: "paralogon" RELATED [] +synonym: "syntenic paralogous to" EXACT [] +xref: RO:HOM0000012 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000012 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with +is_a: in_syntenic_homology_relationship_with ! in syntenic homology relationship with + +[Typedef] +id: in_tandem_paralogy_relationship_with +name: in tandem paralogy relationship with +def: "Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000055, ISBN:978-0878932665] +synonym: "iterative paralogy" RELATED [] +synonym: "serial paralogy" RELATED [] +synonym: "tandem paralogous to" EXACT [] +xref: RO:HOM0000055 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000055 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with + +[Typedef] +id: in_taxon +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +xref: RO:0002162 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +range: CARO:0001010 +is_a: evolutionarily_related_to ! evolutionarily related to + +[Typedef] +id: in_within-species_paralogy_relationship_with +name: in within-species paralogy relationship with +def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "within-species paralogous to" EXACT [] +xref: RO:HOM0000049 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000049 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with +disjoint_from: in_between-species_paralogy_relationship_with ! in between-species paralogy relationship with + +[Typedef] +id: in_xenology_relationship_with +name: in xenology relationship with +def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000018] +comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). +synonym: "xenologous to" EXACT [] +xref: RO:HOM0000018 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000018 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: only_in_taxon +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +xref: RO:0002160 +property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: in_taxon ! in taxon + +[Typedef] +id: serially_homologous_to +name: serially homologous to +xref: RO:0002159 +property_value: IAO:0000114 IAO:0000125 +is_symmetric: true +is_transitive: true +is_a: evolutionarily_related_to ! evolutionarily related to + +[Typedef] +id: shares_ancestor_with +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +xref: RO:0002158 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string +is_symmetric: true +is_transitive: true +is_a: evolutionarily_related_to ! evolutionarily related to diff --git a/src/ontology/subsets/ro-hom.owl b/src/ontology/subsets/ro-hom.owl index f7e98059..3a039acb 100644 --- a/src/ontology/subsets/ro-hom.owl +++ b/src/ontology/subsets/ro-hom.owl @@ -1,6 +1,7 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -58,15 +137,1907 @@ + + + + + + + + d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + ancestral_stucture_of + evolutionarily_descended_from + RO:0002156 + derived_by_descent_from + derived by descent from + + + + + + + + + + + inverse of derived by descent from + RO:0002157 + + has_derived_by_descendant + has derived by descendant + + + + + + + + + + + + two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + Consider obsoleting and merging with child relation, 'in homology relationship with' + RO:0002158 + shares_ancestor_with + VBO calls this homologous_to + shares ancestor with + + + + + + + + + + + + RO:0002159 + serially_homologous_to + serially homologous to + + + + + + + + + lactation SubClassOf 'only in taxon' some 'Mammalia' + + x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. + + 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria + + + + RO:0002160 + only_in_taxon + only in taxon + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + + + + + RO:0002162 + + in_taxon + Connects a biological entity to its taxon of origin. + in taxon + + + + + + + + + + + RO:0002312 + evolutionary_variant_of + evolutionary variant of + + + + + + + + A relationship that holds via some environmental process + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + RO:0002320 + evolutionarily_related_to + evolutionarily related to + + + + + + + + + false + + x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat + + + has fused element + RO:0002374 + derived_from_ancestral_fusion_of + A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. + derived from ancestral fusion of + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. TODO: Add homeomorphy axiom + + + ECO:0000041 RO:HOM0000000 + SO:similar_to + sameness + similar to + correspondence + resemblance in_similarity_relationship_with + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + + + + + + + + + + + + Similarity that results from common evolutionary origin. + + + RO:HOM0000001 + homologous to + in_homology_relationship_with + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + + + + + + + + + + + + + Similarity that results from independent evolution. + + + RO:HOM0000002 + homoplasous to + analogy + in_homoplasy_relationship_with + in homoplasy relationship with + + + + + + Similarity that results from independent evolution. + + + + + + + + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + ECO:0000075 + RO:HOM0000003 + homocracous to + in_homocracy_relationship_with + Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + in homocracy relationship with + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + + + + + + + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + RO:HOM0000004 + analogy + in_convergence_relationship_with + Convergence usually implies a notion of adaptation. + in convergence relationship with + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + + + + + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + RO:HOM0000005 + parallel evolution + in_parallelism_relationship_with + Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + in parallelism relationship with + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + + + + + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + ECO:0000071 + MI:2163 + RO:HOM0000006 + structural homologous to + idealistic homology + in_structural_homology_relationship_with + in structural homology relationship with + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by common descent. + + + homology + ECO:0000080 + RO:HOM0000007 + RO_proposed_relation:homologous_to + SO:0000330 + SO:0000853 + SO:0000857 + SO:homologous_to + TAO:homologous_to + cladistic homology + historical homologous to + phylogenetic homology + taxic homology + true homology + in_historical_homology_relationship_with + in historical homology relationship with + + + + + + Homology that is defined by common descent. + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + ECO:0000067 + RO:HOM0000008 + biological homologous to + transformational homology + in_biological_homology_relationship_with + Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + in biological homology relationship with + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + + + + + + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + RO:HOM0000009 + atavism + rudiment + reversion + in_reversal_relationship_with + in reversal relationship with + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + + + + + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + + MeSH:Synteny + RO:HOM0000010 + SO:0000860 + SO:0005858 + syntenic homologous to + synteny + in_syntenic_homology_relationship_with + in syntenic homology relationship with + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + MeSH:Synteny + + + + + + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + RO:HOM0000011 + SO:0000854 + SO:0000859 + SO:paralogous_to + paralogous to + in_paralogy_relationship_with + in paralogy relationship with + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + + + + + + + + + + + + + Paralogy that involves sets of syntenic blocks. + + + RO:HOM0000012 + syntenic paralogous to + duplicon + paralogon + in_syntenic_paralogy_relationship_with + in syntenic paralogy relationship with + + + + + + Paralogy that involves sets of syntenic blocks. + + + DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y + + + + + + + + + + Syntenic homology that involves chromosomes of different species. + + + RO:HOM0000013 + syntenic orthologous to + in_syntenic_orthology_relationship_with + in syntenic orthology relationship with + + + + + + Syntenic homology that involves chromosomes of different species. + + + + + + + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + + RO:HOM0000014 + fractional homology + partial homologous to + segmental homology + mixed homology + modular homology + partial correspondence + percent homology + in_partial_homology_relationship_with + in partial homology relationship with + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + ISBN:0123195837 + ISBN:978-0471984931 + + + + + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + MeSH:Structural_Homology,_Protein + RO:HOM0000015 + protein structural homologous to + in_protein_structural_homology_relationship_with + in protein structural homology relationship with + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + + + + + + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + + pseudogene + RO:HOM0000016 + SO:non_functional_homolog_of + non functional homologous to + in_non_functional_homology_relationship_with + in non functional homology relationship with + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + SO:non_functional_homolog_of + + + + + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + ECO:00000060 + RO:HOM0000017 + SO:0000855 + SO:0000858 + SO:orthologous_to + orthologous to + in_orthology_relationship_with + The term is sometimes also used for anatomical structures. + in orthology relationship with + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + + + + + + + + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + RO:HOM0000018 + xenologous to + in_xenology_relationship_with + The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + in xenology relationship with + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + + + + + + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + + RO:HOM0000019 + 1 to 1 homologous to + 1:1 homology + one-to-one homology + in_1_to_1_homology_relationship_with + in 1 to 1 homology relationship with + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + BGEE:curator + + + + + + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + RO:HOM0000020 + 1 to 1 orthologous to + 1:1 orthology + one-to-one orthology + in_1_to_1_orthology_relationship_with + in 1 to 1 orthology relationship with + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + + + + + + + + + + + Paralogy that results from a whole genome duplication event. + + + RO:HOM0000022 + ohnologous to + homoeology + in_ohnology_relationship_with + in ohnology relationship with + + + + + + Paralogy that results from a whole genome duplication event. + + + + + + + + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + RO:HOM0000023 + in-paralogous to + inparalogy + symparalogy + in_in-paralogy_relationship_with + in in-paralogy relationship with + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + + + + + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + RO:HOM0000024 + alloparalogy + out-paralogous to + outparalogy + in_out-paralogy_relationship_with + in out-paralogy relationship with + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + + + + + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + RO:HOM0000025 + pro-orthologous to + in_pro-orthology_relationship_with + in pro-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + + + + + + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + RO:HOM0000026 + semi-orthologous to + in_semi-orthology_relationship_with + The converse of pro-orthologous. + in semi-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + + + + + + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + RO:HOM0000027 + serial homologous to + homonomy + in_serial_homology_relationship_with + in serial homology relationship with + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + + + + + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + + RO:HOM0000028 + heterochronous homologous to + heterochrony + in_heterochronous_homology_relationship_with + in heterochronous homology relationship with + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + ISBN:978-0674639416 + + + + + + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + RO:HOM0000029 + juvenification + pedomorphosis + in_paedomorphorsis_relationship_with + in paedomorphorsis relationship with + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + ISBN:978-0674639416 + + + + + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + RO:HOM0000030 + in_peramorphosis_relationship_with + in peramorphosis relationship with + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + + + + + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + RO:HOM0000031 + in_progenesis_relationship_with + in progenesis relationship with + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + ISBN:978-0674639416 + + + + + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + RO:HOM0000032 + juvenilization + neotenous to + in_neoteny_relationship_with + in neoteny relationship with + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + ISBN:978-0674639416 + + + + + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + RO:HOM0000033 + mimicrous to + in_mimicry_relationship_with + in mimicry relationship with + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + + + + + + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + RO:HOM0000034 + 1 to many orthologous to + 1:many orthology + one-to-many orthology + co-orthology + many to 1 orthology + in_1_to_many_orthology_relationship_with + in 1 to many orthology relationship with + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + + + + + + + + + + + Historical homology that involves two members of a larger set of homologs. + + + RO:HOM0000036 + many to many homologous to + many-to-many homology + many:many homology + in_many_to_many_homology_relationship_with + in many to many homology relationship with + + + + + + Historical homology that involves two members of a larger set of homologs. + + + + + + + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + + RO:HOM0000037 + 1 to many homologous to + one-to-many homology + 1:many homology + in_1_to_many_homology_relationship_with + in 1 to many homology relationship with + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + BGEE:curator + + + + + + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + + RO:HOM0000042 + apomorphous to + synapomorphy + in_apomorphy_relationship_with + in apomorphy relationship with + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + ISBN:978-0252068140 + + + + + + + + + + Historical homology that is based on distant shared ancestry. + + + RO:HOM0000043 + plesiomorphous to + symplesiomorphy + in_plesiomorphy_relationship_with + This term is usually contrasted to apomorphy. + in plesiomorphy relationship with + + + + + + Historical homology that is based on distant shared ancestry. + + ISBN:978-0252068140 + + + + + + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + RO:HOM0000044 + deep genetic homology + deep homologous to + generative homology + homoiology + in_deep_homology_relationship_with + Used for structures in distantly related taxa. + in deep homology relationship with + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + + + + + + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + RO:HOM0000045 + hemiplasous to + in_hemiplasy_relationship_with + in hemiplasy relationship with + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + + + + + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + RO:HOM0000046 + gametologous to + in_gametology_relationship_with + in gametology relationship with + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + + + + + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + + MeSH:Chromosome_Pairing + RO:HOM0000047 + chromosomal homologous to + in_chromosomal_homology_relationship_with + in chromosomal homology relationship with + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + ISBN:0195307615 + + + + + + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + RO:HOM0000048 + many to many orthologous to + many-to-many orthology + many:many orthology + trans-orthology + co-orthology + trans-homology + in_many_to_many_orthology_relationship_with + in many to many orthology relationship with + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + + + + + + + + + + + + Paralogy that involves genes from the same species. + + + RO:HOM0000049 + within-species paralogous to + in_within-species_paralogy_relationship_with + in within-species paralogy relationship with + + + + + + Paralogy that involves genes from the same species. + + + + + + + + + + + + Paralogy that involves genes from different species. + + + RO:HOM0000050 + between-species paralogous to + in_between-species_paralogy_relationship_with + The genes have diverged before a speciation event. + in between-species paralogy relationship with + + + + + + Paralogy that involves genes from different species. + + + + + + + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + RO:HOM0000051 + post-displacement + in_postdisplacement_relationship_with + in postdisplacement relationship with + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + + + + + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + RO:HOM0000052 + in_hypermorphosis_relationship_with + in hypermorphosis relationship with + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + ISBN:978-0674639416 + + + + + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + RO:HOM0000053 + synologous to + in_synology_relationship_with + in synology relationship with + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + + + + + + + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + ECO:0000080 + RO:HOM0000054 + isoorthologous to + in_isoorthology_relationship_with + in isoorthology relationship with + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + RO:HOM0000055 + tandem paralogous to + iterative paralogy + serial paralogy + in_tandem_paralogy_relationship_with + in tandem paralogy relationship with + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + ISBN:978-0878932665 + + + + + + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + RO:HOM0000057 + apomorphic tendency + cryptic homology + latent homologous to + underlying synapomorphy + homoiology + homoplastic tendency + re-awakening + in_latent_homology_relationship_with + Used for structures in closely related taxa. + in latent homology relationship with + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + + + ISBN:0199141118 + + + + + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + RO:HOM0000058 + generative homology + syngenous to + in_syngeny_relationship_with + Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + in syngeny relationship with + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R + + + + + + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + RO:HOM0000060 + 1:1 paralogy + apparent 1:1 orthology + apparent orthologous to + pseudoorthology + in_apparent_orthology_relationship_with + The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + in apparent orthology relationship with + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + + + + + + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + RO:HOM0000061 + pseudoparalogous to + in_pseudoparalogy_relationship_with + These genes may come out as paralogs in a single-genome analysis. + in pseudoparalogy relationship with + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + + + + + + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + RO:HOM0000062 + equivalogous to + in_equivalogy_relationship_with + This may include examples of orthology, paralogy and xenology. + in equivalogy relationship with + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + RO:HOM0000063 + interologous to + in_interology_relationship_with + in interology relationship with + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + + + + + + + + + + + Similarity that is characterized by interchangeability in function. + + + RO:HOM0000065 + functional similarity + in_functional_equivalence_relationship_with + in functional equivalence relationship with + + + + + Similarity that is characterized by interchangeability in function. + + + + + + + + + + + + + Biological homology that involves parts of the same organism. + + + RO:HOM0000066 + iterative homologous to + in_iterative_homology_relationship_with + in iterative homology relationship with + + + + + + Biological homology that involves parts of the same organism. + + + + + + + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + RO:HOM0000068 + duplicate xenology + multiple xenology + paraxenologous to + in_paraxenology_relationship_with + in paraxenology relationship with + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + + + + + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + RO:HOM0000069 + plerologous to + in_plerology_relationship_with + This phenomenon is usually due to gene conversion process. + in plerology relationship with + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + + + + + + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + RO:HOM0000071 + homotopous to + in_homotopy_relationship_with + Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + in homotopy relationship with + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + + ISBN:0123195837 + + + + + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + RO:HOM0000072 + heterotopy + in_homeosis_relationship_with + in homeosis relationship with + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + + + + + + + + + + + + Synology that results from allopolyploidy. + + + RO:HOM0000073 + homoeologous to + in_homoeology_relationship_with + On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + in homoeology relationship with + + + + + + Synology that results from allopolyploidy. + + + + + + + + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + RO:HOM0000074 + axis paramorphism + in_paramorphism_relationship_with + in paramorphism relationship with + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + + + + + + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + RO:HOM0000075 + regulogous to + in_regulogy_relationship_with + in regulogy relationship with + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-hom.tsv b/src/ontology/subsets/ro-hom.tsv new file mode 100644 index 00000000..9e64d1bd --- /dev/null +++ b/src/ontology/subsets/ro-hom.tsv @@ -0,0 +1,2 @@ +?x ?label + diff --git a/src/ontology/subsets/ro-interaction.json b/src/ontology/subsets/ro-interaction.json new file mode 100644 index 00000000..67569205 --- /dev/null +++ b/src/ontology/subsets/ro-interaction.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-interaction.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_2D_boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_2D_boundary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "lbl" : "electrically_synapsed_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions." + }, + "xrefs" : [ { + "val" : "RO:0002003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "electrically_synapsed_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002007" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "lbl" : "coincident with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." + }, + "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002008" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note from NCEAS meeting: consider changing primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "coincident_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "lbl" : "regulates in other organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "xrefs" : [ { + "val" : "RO:0002010" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_in_other_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "lbl" : "occurrent part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A part of relation that applies only between occurrents." + }, + "xrefs" : [ { + "val" : "RO:0002012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurrent_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." + }, + "xrefs" : [ { + "val" : "RO:0002013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "xrefs" : [ { + "val" : "RO:0002014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_negative_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], + "xrefs" : [ { + "val" : "RO:0002015" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_positive_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "lbl" : "has necessary component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], + "xrefs" : [ { + "val" : "RO:0002016" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_necessary_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], + "xrefs" : [ { + "val" : "RO:0002017" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:44:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "xrefs" : [ { + "val" : "RO:0002018" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "lbl" : "has ligand", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." + }, + "xrefs" : [ { + "val" : "RO:0002019" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-19T17:30:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ligand" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "lbl" : "transports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." + }, + "xrefs" : [ { + "val" : "RO:0002020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:11:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." + }, + "xrefs" : [ { + "val" : "RO:0002021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "xrefs" : [ { + "val" : "RO:0002022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:38Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. 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No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." + }, + "xrefs" : [ { + "val" : "RO:0002104" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : 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"synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002106" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that 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it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002113" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "synapses in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_presynaptic_terminal_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002114", + "lbl" : "synapsed_via_type_III_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." + }, + "comments" : [ "Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002114" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_via_type_III_bouton_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002115", + "lbl" 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 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}, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002297" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002298" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_morphogenesis_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_maturation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002300" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_disappearance_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002301" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_regression_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002302" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_treated_by_substance" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002303" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_habitat" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002304" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002305" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002309" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stimulus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002313" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports_or_maintains_localization_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "xrefs" : [ { + "val" : "RO:0002314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : 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"http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_acquisition_of_features_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002321" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "colocalizes_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002326" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002327" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enables" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "xrefs" : [ { + "val" : "RO:0002328" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "functionally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "xrefs" : [ { + "val" : "RO:0002329" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_structure_that_is_capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "xrefs" : [ { + "val" : "RO:0002331" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "xrefs" : [ { + "val" : "RO:0002332" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_levels_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002333" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enabled_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002334" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002335" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002336" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "xrefs" : [ { + "val" : "RO:0002337" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_localization_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002338" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002339" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002340" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "imports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "xrefs" : [ { + "val" : "RO:0002341" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_along" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002342" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002343" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_growth_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002344" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' 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"http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "exports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002348", + "lbl" : "results in commitment to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002348" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. 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It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. 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"RO:0002445" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitized_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. 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We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "subject_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002463" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "target_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002469" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_nutrients_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002470" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "eats" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002471" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_eaten_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002473" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "composed_primarily_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "xrefs" : [ { + "val" : "RO:0002476" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/subsets/ro-interaction.obo b/src/ontology/subsets/ro-interaction.obo index 521beb78..57efd25a 100644 --- a/src/ontology/subsets/ro-interaction.obo +++ b/src/ontology/subsets/ro-interaction.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-interaction -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/src/ontology/subsets/ro-interaction.owl b/src/ontology/subsets/ro-interaction.owl index 1f7b268f..4a151349 100644 --- a/src/ontology/subsets/ro-interaction.owl +++ b/src/ontology/subsets/ro-interaction.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-interaction.tsv b/src/ontology/subsets/ro-interaction.tsv new file mode 100644 index 00000000..352e8a3b --- /dev/null +++ b/src/ontology/subsets/ro-interaction.tsv @@ -0,0 +1,51 @@ +?x ?label +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid1 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid18 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid22 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid26 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid33 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid37 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid40 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid5 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid52 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid58 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid61 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid64 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid67 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-mereotopology.json b/src/ontology/subsets/ro-mereotopology.json new file mode 100644 index 00000000..2e50b0cc --- /dev/null +++ b/src/ontology/subsets/ro-mereotopology.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-mereotopology.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : 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For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "xrefs" : [ { + "val" : "RO:0002085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "di" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "encompasses" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_after" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "xrefs" : [ { + "val" : "RO:0002087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "lbl" : "during which starts", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002215" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "xrefs" : [ { + "val" : "RO:0002216" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "xrefs" : [ { + "val" : "RO:0002219" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002220" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "adjacent_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002221" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounds" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "temporally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002223" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Allen" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002224" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "xrefs" : [ { + "val" : "RO:0002225" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "xrefs" : [ { + "val" : "RO:0002226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + }, + "xrefs" : [ { + "val" : "RO:0002227" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "obligate_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + }, + "xrefs" : [ { + "val" : "RO:0002228" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "facultative_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ends with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002229" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002230" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "finished by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002231" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002232" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002233" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002234" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_output" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + }, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ 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the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : 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It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. 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Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). 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Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "xrefs" : [ { + "val" : "RO:0002372" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_origin" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "xrefs" : [ { + "val" : "RO:0002373" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_insertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "xrefs" : [ { + "val" : "RO:0002375" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "interacts_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002435" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/subsets/ro-mereotopology.obo b/src/ontology/subsets/ro-mereotopology.obo index 33d6e97a..ba745b5e 100644 --- a/src/ontology/subsets/ro-mereotopology.obo +++ b/src/ontology/subsets/ro-mereotopology.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-mereotopology -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/src/ontology/subsets/ro-mereotopology.owl b/src/ontology/subsets/ro-mereotopology.owl index 55296922..6b552729 100644 --- a/src/ontology/subsets/ro-mereotopology.owl +++ b/src/ontology/subsets/ro-mereotopology.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-mereotopology.tsv b/src/ontology/subsets/ro-mereotopology.tsv new file mode 100644 index 00000000..68694895 --- /dev/null +++ b/src/ontology/subsets/ro-mereotopology.tsv @@ -0,0 +1,51 @@ +?x ?label +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid1 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid18 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid22 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid26 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid33 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid37 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid40 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid5 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid52 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid58 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid61 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid64 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid67 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-sequence.json b/src/ontology/subsets/ro-sequence.json new file mode 100644 index 00000000..3d3191dc --- /dev/null +++ b/src/ontology/subsets/ro-sequence.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-sequence.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : 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For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "xrefs" : [ { + "val" : "RO:0002085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "di" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "encompasses" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_after" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "xrefs" : [ { + "val" : "RO:0002087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "lbl" : "during which starts", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002215" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "xrefs" : [ { + "val" : "RO:0002216" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "xrefs" : [ { + "val" : "RO:0002219" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002220" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "adjacent_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002221" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounds" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "temporally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002223" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Allen" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002224" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "xrefs" : [ { + "val" : "RO:0002225" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "xrefs" : [ { + "val" : "RO:0002226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + }, + "xrefs" : [ { + "val" : "RO:0002227" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "obligate_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + }, + "xrefs" : [ { + "val" : "RO:0002228" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "facultative_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ends with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002229" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002230" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "finished by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002231" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002232" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002233" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002234" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_output" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + }, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ 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the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : 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It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. 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Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). 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Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "xrefs" : [ { + "val" : "RO:0002372" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_origin" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "xrefs" : [ { + "val" : "RO:0002373" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_insertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "xrefs" : [ { + "val" : "RO:0002375" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "interacts_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002435" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/subsets/ro-sequence.obo b/src/ontology/subsets/ro-sequence.obo index 3df12e6c..fde68107 100644 --- a/src/ontology/subsets/ro-sequence.obo +++ b/src/ontology/subsets/ro-sequence.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-sequence -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/src/ontology/subsets/ro-sequence.owl b/src/ontology/subsets/ro-sequence.owl index bfa36ffb..4482b19b 100644 --- a/src/ontology/subsets/ro-sequence.owl +++ b/src/ontology/subsets/ro-sequence.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-sequence.tsv b/src/ontology/subsets/ro-sequence.tsv new file mode 100644 index 00000000..8f592795 --- /dev/null +++ b/src/ontology/subsets/ro-sequence.tsv @@ -0,0 +1,51 @@ +?x ?label +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid1 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid18 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid22 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid26 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid33 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid37 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid40 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid5 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid52 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid58 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid61 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid64 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid67 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-time-interval.json b/src/ontology/subsets/ro-time-interval.json new file mode 100644 index 00000000..47bf0880 --- /dev/null +++ b/src/ontology/subsets/ro-time-interval.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-time-interval.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : 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For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "xrefs" : [ { + "val" : "RO:0002085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "di" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "encompasses" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_after" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "xrefs" : [ { + "val" : "RO:0002087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "lbl" : "during which starts", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002215" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "xrefs" : [ { + "val" : "RO:0002216" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "xrefs" : [ { + "val" : "RO:0002219" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002220" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "adjacent_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002221" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounds" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "temporally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002223" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Allen" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002224" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "xrefs" : [ { + "val" : "RO:0002225" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "xrefs" : [ { + "val" : "RO:0002226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + }, + "xrefs" : [ { + "val" : "RO:0002227" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "obligate_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + }, + "xrefs" : [ { + "val" : "RO:0002228" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "facultative_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ends with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002229" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002230" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "finished by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002231" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002232" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002233" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002234" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_output" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + }, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ 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the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : 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It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. 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Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). 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Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "xrefs" : [ { + "val" : "RO:0002372" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_origin" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "xrefs" : [ { + "val" : "RO:0002373" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_insertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "xrefs" : [ { + "val" : "RO:0002375" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "interacts_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002435" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/src/ontology/subsets/ro-time-interval.obo b/src/ontology/subsets/ro-time-interval.obo index 7aeb28f2..8150a607 100644 --- a/src/ontology/subsets/ro-time-interval.obo +++ b/src/ontology/subsets/ro-time-interval.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-time-interval -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/src/ontology/subsets/ro-time-interval.owl b/src/ontology/subsets/ro-time-interval.owl index 85959a1e..286fb05e 100644 --- a/src/ontology/subsets/ro-time-interval.owl +++ b/src/ontology/subsets/ro-time-interval.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/ro-time-interval.tsv b/src/ontology/subsets/ro-time-interval.tsv new file mode 100644 index 00000000..a57fc830 --- /dev/null +++ b/src/ontology/subsets/ro-time-interval.tsv @@ -0,0 +1,51 @@ +?x ?label +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid1 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid18 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid22 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid26 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid33 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid37 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid40 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid5 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid52 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid58 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid61 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid64 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid67 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh new file mode 100644 index 00000000..395ee647 --- /dev/null +++ b/src/scripts/update_repo.sh @@ -0,0 +1,30 @@ +echo "This (experimental) update script will create a new repo according to your config file. It will:" +echo "(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries wont be touched) and docker wrapper (run.sh)." +echo "(2) and add missing files, if any." + +set -e + +OID=ro +ROOTDIR=../.. +SRCDIR=.. +CONFIG=$OID"-odk.yaml" + +rm -rf target +mkdir target +/tools/odk.py seed -c -g -C $CONFIG +ls -l target/$OID/src +ls -l $SRCDIR/ +cp target/$OID/src/scripts/update_repo.sh $SRCDIR/scripts/ +rsync -r -u --ignore-existing --exclude 'patterns/data/default/example.tsv' --exclude 'patterns/dosdp-patterns/example.yaml' target/$OID/src/ $SRCDIR/ +cp target/$OID/src/ontology/Makefile $SRCDIR/ontology/ +cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/ +cp -r target/$OID/src/sparql/* $SRCDIR/sparql/ +mkdir -p $ROOTDIR/.github +mkdir -p $ROOTDIR/.github/workflows +cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml + + + +echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)" +echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml." +echo "Ontology repository update successfully completed." \ No newline at end of file diff --git a/src/scripts/validate_id_ranges.sc b/src/scripts/validate_id_ranges.sc new file mode 100644 index 00000000..1785e8df --- /dev/null +++ b/src/scripts/validate_id_ranges.sc @@ -0,0 +1,75 @@ +import $ivy.`net.sourceforge.owlapi:owlapi-distribution:4.5.16` +import $ivy.`com.outr::scribe-slf4j:2.7.12` +import org.semanticweb.owlapi.apibinding.OWLManager +import org.semanticweb.owlapi.model._ +import org.semanticweb.owlapi.vocab.OWLFacet +import java.io.File +import scala.collection +import scala.collection.mutable +import scala.jdk.CollectionConverters._ +@main +def main(id_range_file: os.Path) = { + val o = OWLManager.createOWLOntologyManager().loadOntology(IRI.create(id_range_file.toIO)) + val allMyFacets = mutable.ListBuffer.empty[MyFacet] + for (dt <- o.getDatatypesInSignature().asScala) { + val defs = o.getAxioms(dt) + for (ax <- defs.asScala) { + val range = ax.getDataRange() + val f = new MyFacet() + f.id = dt.toString() + range.accept(new OWLDataRangeVisitor() { + override + def visit(owlDatatype: OWLDatatype) = () + override + def visit(owlDataOneOf: OWLDataOneOf) = () + override + def visit(owlDataComplementOf: OWLDataComplementOf) = () + override + def visit(owlDataIntersectionOf: OWLDataIntersectionOf) = () + override + def visit(owlDataUnionOf: OWLDataUnionOf) = () + override + def visit(owlDatatypeRestriction: OWLDatatypeRestriction) = { + for (fr <- owlDatatypeRestriction.getFacetRestrictions().asScala) { + var i = fr.getFacetValue().parseInteger() + if(fr.getFacet().equals(OWLFacet.MIN_INCLUSIVE)) { + f.min = i + } else if(fr.getFacet().equals(OWLFacet.MAX_INCLUSIVE)) { + f.max = i + } else if(fr.getFacet().equals(OWLFacet.MIN_EXCLUSIVE)) { + i += 1 + f.min = i + } else if(fr.getFacet().equals(OWLFacet.MAX_EXCLUSIVE)) { + i -= 1 + f.max = i + } else { + log("Unknown range restriction: "+fr) + } + } + } + }) + log("Testing range: "+f) + testFacetViolation(f,allMyFacets) + allMyFacets.append(f) + } + } +} +def testFacetViolation(f: MyFacet , allMyFacets: collection.Seq[MyFacet]) = { + for (f_p <- allMyFacets) { + if (((f.min <= f_p.max) && (f_p.min <= f.max))) { + throw new IllegalStateException(f + " overlaps with " + f_p + "!") + } + } +} +def log(o: Object) = { + println(o.toString()) +} +class MyFacet { + var min: Int = _ + var max: Int = _ + var id: String = _ + override + def toString(): String = { + return "Facet{" + id + "}[min:" + min + " max:" + max + "]" + } +} \ No newline at end of file diff --git a/src/sparql/README.md b/src/sparql/README.md new file mode 100644 index 00000000..87c432e3 --- /dev/null +++ b/src/sparql/README.md @@ -0,0 +1,32 @@ +# Sparql checks + +[SPARQL](https://www.w3.org/TR/rdf-sparql-query/) is a W3C standard +query language for RDF. This directory contains useful SPARQL queries +for perfoming over the ontology. + +SPARQL can be executed on a triplestore or directly on any OWL +file. The queries here are all executed on either ro-edit.obo or +downstream products in the [ontology](../ontology/) folder. We use +`robot` as this allows easy execution over any Obo-format or OWL file. + +We break the queries into 3 categories: + +## Constraint Violation checks + +These are all named `*violation.sparql`. A subset of these are +configured to be executed via travis. If these return any results, +then the build will fail. + +Consult the individual sparql files to see the intent of the check + +## Construct queries + +These are named `construct*.sparql`, and always have the form `CONSTRUCT ...`. + +These are used to generate new OWL axioms that can be inserted back +into the ontology. + +## Reports + +The remaining SPARQL queries are for informative purposes. A subset +may be executed with each release. \ No newline at end of file diff --git a/src/ontology/sparql/addDisjointnessAxioms.sparql b/src/sparql/addDisjointnessAxioms.sparql similarity index 100% rename from src/ontology/sparql/addDisjointnessAxioms.sparql rename to src/sparql/addDisjointnessAxioms.sparql diff --git a/src/ontology/sparql/addMetadataForInverse.sparql b/src/sparql/addMetadataForInverse.sparql similarity index 100% rename from src/ontology/sparql/addMetadataForInverse.sparql rename to src/sparql/addMetadataForInverse.sparql diff --git a/src/sparql/basic-report.sparql b/src/sparql/basic-report.sparql new file mode 100644 index 00000000..cff97737 --- /dev/null +++ b/src/sparql/basic-report.sparql @@ -0,0 +1,12 @@ +prefix oio: +prefix def: +prefix owl: + +SELECT ?cls ?def (group_concat(?xref) as ?xrefs) WHERE +{ + ?cls a owl:Class . + OPTIONAL { ?cls oio:hasDbXref ?xref } . + OPTIONAL { ?cls def: ?def } . + FILTER (!isBlank(?cls)) +} +GROUP BY ?cls ?def diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql new file mode 100644 index 00000000..0c4d2844 --- /dev/null +++ b/src/sparql/class-count-by-prefix.sparql @@ -0,0 +1,10 @@ +prefix owl: +prefix obo: + +SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE +{ + ?cls a owl:Class . + FILTER (!isBlank(?cls)) + BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix) +} +GROUP BY ?prefix diff --git a/src/ontology/sparql/construct-universal-from-homeomorphy.sparql b/src/sparql/construct-universal-from-homeomorphy.sparql similarity index 100% rename from src/ontology/sparql/construct-universal-from-homeomorphy.sparql rename to src/sparql/construct-universal-from-homeomorphy.sparql diff --git a/src/sparql/def-lacks-xref-violation.sparql b/src/sparql/def-lacks-xref-violation.sparql new file mode 100644 index 00000000..cff97737 --- /dev/null +++ b/src/sparql/def-lacks-xref-violation.sparql @@ -0,0 +1,12 @@ +prefix oio: +prefix def: +prefix owl: + +SELECT ?cls ?def (group_concat(?xref) as ?xrefs) WHERE +{ + ?cls a owl:Class . + OPTIONAL { ?cls oio:hasDbXref ?xref } . + OPTIONAL { ?cls def: ?def } . + FILTER (!isBlank(?cls)) +} +GROUP BY ?cls ?def diff --git a/src/ontology/sparql/detectDefinedByInverse.sparql b/src/sparql/detectDefinedByInverse.sparql similarity index 100% rename from src/ontology/sparql/detectDefinedByInverse.sparql rename to src/sparql/detectDefinedByInverse.sparql diff --git a/src/sparql/edges.sparql b/src/sparql/edges.sparql new file mode 100644 index 00000000..edf658bf --- /dev/null +++ b/src/sparql/edges.sparql @@ -0,0 +1,18 @@ +prefix owl: +prefix rdfs: +prefix rdf: + +SELECT ?x ?p ?y +WHERE { + {?x rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty ?p ; + owl:someValuesFrom ?y ] + } + UNION { + ?x rdfs:subClassOf ?y . + BIND(rdfs:subClassOf AS ?p) + } + ?x a owl:Class . + ?y a owl:Class . +} diff --git a/src/sparql/equivalent-classes-violation.sparql b/src/sparql/equivalent-classes-violation.sparql new file mode 100644 index 00000000..ed5ccdd0 --- /dev/null +++ b/src/sparql/equivalent-classes-violation.sparql @@ -0,0 +1,14 @@ +prefix oio: +prefix owl: +prefix rdfs: + +SELECT ?baseClass ?baseLabel ?equivalentClass ?equivalentLabel WHERE +{ + ?baseClass owl:equivalentClass ?equivalentClass . + ?baseClass rdfs:label ?baseLabel . + ?equivalentClass rdfs:label ?equivalentLabel . + + FILTER (!isBlank(?baseClass)) . + FILTER (!isBlank(?equivalentClass)) + +} diff --git a/src/sparql/illegal-date-violation.sparql b/src/sparql/illegal-date-violation.sparql new file mode 100644 index 00000000..25ec6603 --- /dev/null +++ b/src/sparql/illegal-date-violation.sparql @@ -0,0 +1,10 @@ +PREFIX dct: +PREFIX xsd: + +SELECT DISTINCT ?term ?property ?value WHERE +{ + VALUES ?property {dct:date dct:issued dct:created} + ?term ?property ?value . + FILTER (datatype(?value) != xsd:date || !regex(str(?value), '^\\d{4}-\\d\\d-\\d\\d$')) +} + diff --git a/src/sparql/inject-subset-declaration.ru b/src/sparql/inject-subset-declaration.ru new file mode 100644 index 00000000..788313b7 --- /dev/null +++ b/src/sparql/inject-subset-declaration.ru @@ -0,0 +1,11 @@ +PREFIX : +PREFIX rdf: +PREFIX rdfs: + +INSERT { ?y rdfs:subPropertyOf . } + +WHERE { + ?x ?y . + FILTER(isIRI(?y)) + FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://purl.obolibrary.org/obo)")) +} \ No newline at end of file diff --git a/src/sparql/inject-synonymtype-declaration.ru b/src/sparql/inject-synonymtype-declaration.ru new file mode 100644 index 00000000..cad57edb --- /dev/null +++ b/src/sparql/inject-synonymtype-declaration.ru @@ -0,0 +1,11 @@ +PREFIX : +PREFIX rdf: +PREFIX rdfs: + +INSERT { ?y rdfs:subPropertyOf . } + +WHERE { + ?x ?y . + FILTER(isIRI(?y)) + FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://purl.obolibrary.org/obo)")) +} \ No newline at end of file diff --git a/src/sparql/iri-range-advanced-violation.sparql b/src/sparql/iri-range-advanced-violation.sparql new file mode 100644 index 00000000..bf580693 --- /dev/null +++ b/src/sparql/iri-range-advanced-violation.sparql @@ -0,0 +1,21 @@ +PREFIX never_in_taxon: +PREFIX present_in_taxon: +PREFIX oboInOwl: +PREFIX dcterms: +PREFIX rdfs: +PREFIX foaf: + +SELECT ?term ?property ?value +WHERE { + VALUES ?property { + never_in_taxon: + present_in_taxon: + rdfs:seeAlso + foaf:depicted_by + oboInOwl:inSubset + dcterms:contributor } + ?term ?property ?value . + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) + FILTER (!isIRI(?value)) +} + diff --git a/src/sparql/iri-range-violation.sparql b/src/sparql/iri-range-violation.sparql new file mode 100644 index 00000000..66d8e919 --- /dev/null +++ b/src/sparql/iri-range-violation.sparql @@ -0,0 +1,19 @@ +PREFIX never_in_taxon: +PREFIX present_in_taxon: +PREFIX oboInOwl: +PREFIX dcterms: +PREFIX foaf: + +SELECT ?term ?property ?value +WHERE { + VALUES ?property { + never_in_taxon: + present_in_taxon: + foaf:depicted_by + oboInOwl:inSubset + dcterms:contributor } + ?term ?property ?value . + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) + FILTER (!isIRI(?value)) +} + diff --git a/src/sparql/label-with-iri-violation.sparql b/src/sparql/label-with-iri-violation.sparql new file mode 100644 index 00000000..7f701bcb --- /dev/null +++ b/src/sparql/label-with-iri-violation.sparql @@ -0,0 +1,9 @@ +PREFIX rdfs: + +SELECT ?term ?value +WHERE { + ?term rdfs:label ?value . + FILTER (REGEX(?value, "http[s]?[:]")) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) +} + diff --git a/src/sparql/labels.sparql b/src/sparql/labels.sparql new file mode 100644 index 00000000..89e9ec7f --- /dev/null +++ b/src/sparql/labels.sparql @@ -0,0 +1,9 @@ +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: + +SELECT ?x (STR(?lab) AS ?label) WHERE { + ?x rdf:type owl:Class . + OPTIONAL {?x rdfs:label ?lab} +} +ORDER BY ?x diff --git a/src/sparql/multiple-replaced_by-violation.sparql b/src/sparql/multiple-replaced_by-violation.sparql new file mode 100644 index 00000000..65bb8de2 --- /dev/null +++ b/src/sparql/multiple-replaced_by-violation.sparql @@ -0,0 +1,12 @@ +PREFIX replaced_by: + +SELECT DISTINCT ?entity ?property ?value WHERE { + VALUES ?property { + replaced_by: + } + ?entity ?property ?value1 . + ?entity ?property ?value2 . + FILTER(?value1!=?value2) + BIND(CONCAT(str(?value1), CONCAT("|", str(?value2))) as ?value) +} + diff --git a/src/sparql/nolabels-violation.sparql b/src/sparql/nolabels-violation.sparql new file mode 100644 index 00000000..d506a41e --- /dev/null +++ b/src/sparql/nolabels-violation.sparql @@ -0,0 +1,13 @@ +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: + +SELECT ?cls WHERE { + ?cls a owl:Class + FILTER NOT EXISTS {?cls rdfs:label ?lab} + FILTER NOT EXISTS {?cls replaced_by: ?replCls} + FILTER (!isBlank(?cls)) + FILTER ( regex(str(?cls), "^http://purl.obolibrary.org/obo/GO_")) +} +ORDER BY ?cls diff --git a/src/ontology/sparql/objectProperties.sparql b/src/sparql/objectProperties.sparql similarity index 100% rename from src/ontology/sparql/objectProperties.sparql rename to src/sparql/objectProperties.sparql diff --git a/src/sparql/obsolete-violation.sparql b/src/sparql/obsolete-violation.sparql new file mode 100644 index 00000000..c81bf718 --- /dev/null +++ b/src/sparql/obsolete-violation.sparql @@ -0,0 +1,24 @@ +prefix xsd: +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: +PREFIX consider: + +SELECT ?cls ?clsLabel ?rule WHERE { + ?cls a owl:Class ; + rdfs:label ?clsLabel ; + owl:deprecated "true"^^xsd:boolean + { + { + FILTER ( ! regex(str(?clsLabel), "^obsolete ") ) + BIND ("obsolete label must start with obsolete" AS ?rule) + } + UNION + { + ?cls rdfs:subClassOf ?parent + BIND("no logical axioms for obsolete" AS ?rule) + } + } +} +ORDER BY ?cls diff --git a/src/sparql/obsoletes.sparql b/src/sparql/obsoletes.sparql new file mode 100644 index 00000000..7aff433b --- /dev/null +++ b/src/sparql/obsoletes.sparql @@ -0,0 +1,14 @@ +prefix xsd: +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: +PREFIX consider: + +SELECT ?cls ?replCls ?consCls WHERE { + ?cls a owl:Class ; + owl:deprecated "true"^^xsd:boolean . + OPTIONAL {?cls replaced_by: ?replCls} + OPTIONAL {?cls consider: ?consCls} +} +ORDER BY ?cls diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql new file mode 100644 index 00000000..1efed040 --- /dev/null +++ b/src/sparql/owldef-self-reference-violation.sparql @@ -0,0 +1,12 @@ +PREFIX rdf: +PREFIX oio: +PREFIX owl: +PREFIX rdfs: + +SELECT ?term WHERE { + { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] } + UNION + { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] } + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) +} + diff --git a/src/sparql/owldef-violation.sparql b/src/sparql/owldef-violation.sparql new file mode 100644 index 00000000..3b59f882 --- /dev/null +++ b/src/sparql/owldef-violation.sparql @@ -0,0 +1,9 @@ +prefix oio: +prefix owl: +prefix rdfs: + +WELECT * +WHERE { + ?c rdfs:subClassOf ?d ; + owl:equivalentClass [ + owl:intersectionOf TODO diff --git a/src/sparql/postprocess-module.ru b/src/sparql/postprocess-module.ru new file mode 100644 index 00000000..0767af1e --- /dev/null +++ b/src/sparql/postprocess-module.ru @@ -0,0 +1,16 @@ +PREFIX rdf: +PREFIX rdfs: +PREFIX dc: +PREFIX owl: + + +DELETE { + ?ontology ?ontology_annotation_property ?ontology_annotation_value . +} + +WHERE { + ?ontology rdf:type owl:Ontology . + ?ontology ?ontology_annotation_property ?ontology_annotation_value . + FILTER(?ontology_annotation_property != dc:source && ?ontology_annotation_property != rdf:type) + +} \ No newline at end of file diff --git a/src/sparql/preprocess-module.ru b/src/sparql/preprocess-module.ru new file mode 100644 index 00000000..99120a0c --- /dev/null +++ b/src/sparql/preprocess-module.ru @@ -0,0 +1,22 @@ +PREFIX rdf: +PREFIX rdfs: +PREFIX dc: +PREFIX owl: + + +#DELETE { +# ?ontology ?ontology_annotation_property ?ontology_annotation_value . +#} + +INSERT { + ?ontology dc:source ?version_iri . +} + +WHERE { + ?ontology rdf:type owl:Ontology ; + owl:versionIRI ?version_iri . + #OPTIONAL { + # ?ontology ?ontology_annotation_property ?ontology_annotation_value . + #} + +} \ No newline at end of file diff --git a/src/sparql/redundant-subClassOf-violation.sparql b/src/sparql/redundant-subClassOf-violation.sparql new file mode 100644 index 00000000..e8cba8e9 --- /dev/null +++ b/src/sparql/redundant-subClassOf-violation.sparql @@ -0,0 +1,15 @@ +PREFIX oio: +PREFIX owl: +PREFIX rdfs: + +SELECT ?term ?xl ?y ?yl ?z ?zl WHERE { + ?term rdfs:subClassOf ?y ; + rdfs:label ?xl . + ?y rdfs:subClassOf+ ?z ; + rdfs:label ?yl . + ?term rdfs:subClassOf ?z . + ?z rdfs:label ?zl . + + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) +} + diff --git a/src/sparql/ro_terms.sparql b/src/sparql/ro_terms.sparql new file mode 100644 index 00000000..40179a04 --- /dev/null +++ b/src/sparql/ro_terms.sparql @@ -0,0 +1,7 @@ +SELECT DISTINCT ?term +WHERE { + { ?s1 ?p1 ?term . } + UNION + { ?term ?p2 ?o2 . } + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) +} diff --git a/src/sparql/simple-seed.sparql b/src/sparql/simple-seed.sparql new file mode 100644 index 00000000..247fbde8 --- /dev/null +++ b/src/sparql/simple-seed.sparql @@ -0,0 +1,13 @@ +prefix owl: + +SELECT DISTINCT ?cls WHERE +{ + {?cls a owl:AnnotationProperty .} + UNION + {?cls a owl:ObjectProperty .} + UNION + {?x ?cls} + UNION + {?x ?cls} + FILTER (!isBlank(?cls)) +} diff --git a/src/sparql/subsets-labeled.sparql b/src/sparql/subsets-labeled.sparql new file mode 100644 index 00000000..5ca7e31c --- /dev/null +++ b/src/sparql/subsets-labeled.sparql @@ -0,0 +1,13 @@ +prefix oio: +prefix owl: +prefix inSubset: +prefix rdfs: + +SELECT ?subset ?clsLabel +WHERE +{ + ?cls a owl:Class ; + inSubset: ?subset ; + rdfs:label ?clsLabel +} +ORDER BY ?subset ?cls diff --git a/src/sparql/synonyms.sparql b/src/sparql/synonyms.sparql new file mode 100644 index 00000000..ba6b03a7 --- /dev/null +++ b/src/sparql/synonyms.sparql @@ -0,0 +1,26 @@ +prefix owl: +prefix oboInOwl: +prefix rdfs: + +SELECT ?cls ?pred ?val ?synType +WHERE + { ?cls ?pred ?val ; + a owl:Class . + FILTER ( + ?pred = rdfs:label || + ?pred = oboInOwl:hasRelatedSynonym || + ?pred = oboInOwl:hasNarrowSynonym || + ?pred = oboInOwl:hasBroadSynonym || + ?pred = oboInOwl:hasExactSynonym + ) + + OPTIONAL { + [ + a owl:Axiom ; + owl:annotatedSource ?cls ; + owl:annotatedProperty ?pred ; + owl:annotatedTarget ?val ; + oboInOwl:hasSynonymType ?synType + ] + } + } diff --git a/src/sparql/taxon-range-violation.sparql b/src/sparql/taxon-range-violation.sparql new file mode 100644 index 00000000..c31353d5 --- /dev/null +++ b/src/sparql/taxon-range-violation.sparql @@ -0,0 +1,11 @@ +PREFIX never_in_taxon: +PREFIX present_in_taxon: + +SELECT ?term ?property ?taxon +WHERE { + VALUES ?property { never_in_taxon: present_in_taxon: } + ?term ?property ?taxon . + FILTER (!isIRI(?taxon) || !STRSTARTS(STR(?taxon), "http://purl.obolibrary.org/obo/NCBITaxon_")) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/RO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000050") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000051") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BFO_0000060"))) +} + diff --git a/src/sparql/term-tracker-uri-violation.sparql b/src/sparql/term-tracker-uri-violation.sparql new file mode 100644 index 00000000..6fbd9938 --- /dev/null +++ b/src/sparql/term-tracker-uri-violation.sparql @@ -0,0 +1,9 @@ +PREFIX xsd: +PREFIX term_tracker_item: + +SELECT ?term ?term_tracker ?term_tracker_type WHERE { + ?term term_tracker_item: ?term_tracker . + FILTER(DATATYPE(?term_tracker) != xsd:anyURI) + BIND(DATATYPE(?term_tracker) as ?term_tracker_type) +} + diff --git a/src/sparql/terms.sparql b/src/sparql/terms.sparql new file mode 100644 index 00000000..ec58b4ca --- /dev/null +++ b/src/sparql/terms.sparql @@ -0,0 +1,15 @@ +PREFIX rdf: +prefix owl: +SELECT DISTINCT ?term +WHERE { + { + ?s1 ?p1 ?term . + FILTER(?p1!=rdf:type) + } + UNION + { + ?term ?p2 ?o2 . + FILTER(?o2!=owl:Ontology) + } + FILTER(isIRI(?term)) +} \ No newline at end of file diff --git a/src/sparql/xrefs.sparql b/src/sparql/xrefs.sparql new file mode 100644 index 00000000..bde8fc98 --- /dev/null +++ b/src/sparql/xrefs.sparql @@ -0,0 +1,8 @@ +prefix oio: +prefix owl: + +SELECT ?cls ?xref WHERE +{ + ?cls a owl:Class ; + oio:hasDbXref ?xref +} diff --git a/subsets/ro-biotic-interaction.json b/subsets/ro-biotic-interaction.json new file mode 100644 index 00000000..8309ba7d --- /dev/null +++ b/subsets/ro-biotic-interaction.json @@ -0,0 +1,1137 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002437", + "lbl" : "biotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "interacts with on organism level" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/interactsWith" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002438", + "lbl" : "trophically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the partners are related via a feeding relationship." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "lbl" : "preys on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Baleen whale preys on krill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7134-3324" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of predation interaction with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preys upon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/preysUpon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.inaturalist.org/observations/2942824" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002440", + "lbl" : "symbiotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction in which the two organisms live together in more or less intimate association." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002441", + "lbl" : "commensually interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002442", + "lbl" : "mutualistically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "lbl" : "interacts with via parasite-host interaction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002444", + "lbl" : "parasite of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "direct parasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Pediculus humanus capitis parasite of human" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitizes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/parasitizes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002445", + "lbl" : "parasitized by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "directly parasitized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "semibiotically interacts with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Porifiera attaches to substrate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002453", + "lbl" : "host of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "lbl" : "has host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasHost" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002455", + "lbl" : "pollinates", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Bees pollinate Flowers" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/pollinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "lbl" : "pollinated by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has polinator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasPollinator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "lbl" : "acquires nutrients from", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002458", + "lbl" : "preyed upon by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of preys on" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has predator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of predation interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/HasPredator" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "lbl" : "is vector for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002460", + "lbl" : "has vector", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002553", + "lbl" : "hyperparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "hyperparasitoid of" + }, { + "pred" : "hasRelatedSynonym", + "val" : "epiparasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://eol.org/schema/terms/hyperparasitoidOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Hyperparasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "lbl" : "hyperparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of hyperparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "has epiparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has hyperparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hyperparasitoidized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002555", + "lbl" : "allelopath of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Allelopathy" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/allelopathyYes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002556", + "lbl" : "pathogen of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002557", + "lbl" : "has pathogen", + "type" : 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"http://purl.obolibrary.org/obo/RO_0002633" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002634", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002635" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002636", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002637" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002638", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002639" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002640", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002641" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008501", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0008502" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008503", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0008504" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0008507", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0008508" + } ], + "propertyChainAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002553", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002444", "http://purl.obolibrary.org/obo/RO_0002444" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002554", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002445", "http://purl.obolibrary.org/obo/RO_0002445" ] + } ] + } ] +} \ No newline at end of file diff --git a/subsets/ro-biotic-interaction.obo b/subsets/ro-biotic-interaction.obo new file mode 100644 index 00000000..1f33ac3f --- /dev/null +++ b/subsets/ro-biotic-interaction.obo @@ -0,0 +1,486 @@ +format-version: 1.2 +ontology: ro + +[Typedef] +id: RO:0002208 +name: parasitoid of +def: "A parasite that kills or sterilizes its host" [] +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002209 ! has parasitoid + +[Typedef] +id: RO:0002209 +name: has parasitoid +def: "inverse of parasitoid of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002227 +name: obligate parasite of +def: "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002228 +name: facultative parasite of +def: "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002235 +name: stem parasite of +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002236 +name: root parasite of +def: "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002237 +name: hemiparasite of +def: "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." [] +is_a: RO:0002444 ! parasite of + +[Typedef] +id: RO:0002437 +name: biotically interacts with +def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "interacts with on organism level" xsd:string +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string +is_symmetric: true + +[Typedef] +id: RO:0002438 +name: trophically interacts with +def: "An interaction relationship in which the partners are related via a feeding relationship." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002439 +name: preys on +def: "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" [] +subset: ro-eco +property_value: IAO:0000112 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" xsd:string +property_value: IAO:0000112 "Baleen whale preys on krill" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7134-3324 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 +property_value: IAO:0000118 "is subject of predation interaction with" xsd:string +property_value: IAO:0000118 "preys upon" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string +is_a: RO:0002438 ! trophically interacts with +inverse_of: RO:0002458 ! preyed upon by + +[Typedef] +id: RO:0002440 +name: symbiotically interacts with +def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string +is_symmetric: true +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002441 +name: commensually interacts with +def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002442 +name: mutualistically interacts with +def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002443 +name: interacts with via parasite-host interaction +def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI +property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002444 +name: parasite of +subset: ro-eco +synonym: "direct parasite of" EXACT [] +property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "parasitizes" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string +is_a: RO:0002443 ! interacts with via parasite-host interaction +is_a: RO:0002454 ! has host +inverse_of: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002445 +name: parasitized by +subset: ro-eco +synonym: "directly parasitized by" EXACT [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has parasite" xsd:string +property_value: IAO:0000118 "parasitised by" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string +is_a: RO:0002443 ! interacts with via parasite-host interaction +is_a: RO:0002453 ! host of + +[Typedef] +id: RO:0002446 +name: participates in a abiotic-biotic interaction with +def: "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." [] +subset: ro-eco +synonym: "semibiotically interacts with" RELATED [] +property_value: IAO:0000112 "Porifiera attaches to substrate" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +is_a: RO:0002437 ! biotically interacts with + +[Typedef] +id: RO:0002453 +name: host of +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002454 +name: has host +def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0002455 +name: pollinates +subset: ro-eco +property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string +property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string +is_a: RO:0002442 ! mutualistically interacts with +inverse_of: RO:0002456 ! pollinated by + +[Typedef] +id: RO:0002456 +name: pollinated by +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has polinator" xsd:string +property_value: IAO:0000118 "is target of pollination interaction with" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string +is_a: RO:0002442 ! mutualistically interacts with + +[Typedef] +id: RO:0002457 +name: acquires nutrients from +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string +is_a: RO:0002438 ! trophically interacts with +inverse_of: RO:0002469 ! provides nutrients for + +[Typedef] +id: RO:0002458 +name: preyed upon by +def: "inverse of preys on" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "has predator" xsd:string +property_value: IAO:0000118 "is target of predation interaction with" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002459 +name: is vector for +subset: ro-eco +property_value: IAO:0000112 "Anopheles is a vector for Plasmodium" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" xsd:string +is_a: RO:0002574 ! participates in a biotic-biotic interaction with +inverse_of: RO:0002460 ! has vector + +[Typedef] +id: RO:0002460 +name: has vector +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002469 +name: provides nutrients for +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002470 +name: eats +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "is subject of eating interaction with" xsd:string +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002471 +name: is eaten by +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "eaten by" xsd:string +property_value: IAO:0000118 "is target of eating interaction with" xsd:string +is_a: RO:0002438 ! trophically interacts with + +[Typedef] +id: RO:0002553 +name: hyperparasite of +def: "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" [] +subset: ro-eco +synonym: "epiparasite of" RELATED [] +synonym: "hyperparasitoid of" NARROW [] +property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string +holds_over_chain: RO:0002444 RO:0002444 +is_a: RO:0002454 ! has host +inverse_of: RO:0002554 ! hyperparasitized by + +[Typedef] +id: RO:0002554 +name: hyperparasitized by +def: "inverse of hyperparasite of" [] +subset: ro-eco +subset: RO:0002259 +synonym: "has epiparasite" RELATED [] +synonym: "has hyperparasite" RELATED [] +synonym: "hyperparasitoidized by" RELATED [] +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +holds_over_chain: RO:0002445 RO:0002445 +is_a: RO:0002453 ! host of + +[Typedef] +id: RO:0002555 +name: allelopath of +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string +property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002556 +name: pathogen of +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002454 ! has host +inverse_of: RO:0002557 ! has pathogen + +[Typedef] +id: RO:0002557 +name: has pathogen +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002453 ! host of + +[Typedef] +id: RO:0002574 +name: participates in a biotic-biotic interaction with +subset: ro-eco +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 +is_a: RO:0002437 ! biotically interacts with + +[Typedef] +id: RO:0002618 +name: visits +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI +is_a: RO:0002574 ! participates in a biotic-biotic interaction with +inverse_of: RO:0002619 ! visited by + +[Typedef] +id: RO:0002619 +name: visited by +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002622 +name: visits flowers of +is_a: RO:0002618 ! visits +inverse_of: RO:0002623 ! has flowers visited by + +[Typedef] +id: RO:0002623 +name: has flowers visited by +is_a: RO:0002619 ! visited by + +[Typedef] +id: RO:0002624 +name: lays eggs in +is_a: RO:0002444 ! parasite of +is_a: RO:0002618 ! visits +inverse_of: RO:0002625 ! has eggs laid in by + +[Typedef] +id: RO:0002625 +name: has eggs laid in by +is_a: RO:0002445 ! parasitized by +is_a: RO:0002619 ! visited by + +[Typedef] +id: RO:0002626 +name: kills +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string +is_a: RO:0002574 ! participates in a biotic-biotic interaction with +inverse_of: RO:0002627 ! is killed by + +[Typedef] +id: RO:0002627 +name: is killed by +is_a: RO:0002574 ! participates in a biotic-biotic interaction with + +[Typedef] +id: RO:0002632 +name: ectoparasite of +def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] +property_value: IAO:0000119 Types +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002633 ! has ectoparasite + +[Typedef] +id: RO:0002633 +name: has ectoparasite +def: "inverse of ectoparasite of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002634 +name: endoparasite of +synonym: "lives inside of" RELATED [] +property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string +property_value: IAO:0000119 Types +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002635 ! has endoparasite + +[Typedef] +id: RO:0002635 +name: has endoparasite +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002636 +name: mesoparasite of +def: "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" [] +is_a: RO:0002444 ! parasite of +inverse_of: RO:0002637 ! has mesoparasite + +[Typedef] +id: RO:0002637 +name: has mesoparasite +def: "inverse of mesoparasite of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0002638 +name: intercellular endoparasite of +def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] +property_value: IAO:0000119 Types +is_a: RO:0002634 ! endoparasite of +inverse_of: RO:0002639 ! has intercellular endoparasite + +[Typedef] +id: RO:0002639 +name: has intercellular endoparasite +def: "inverse of intercellular endoparasite of" [] +subset: RO:0002259 +is_a: RO:0002635 ! has endoparasite + +[Typedef] +id: RO:0002640 +name: intracellular endoparasite of +def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] +property_value: IAO:0000119 Types +is_a: RO:0002634 ! endoparasite of +inverse_of: RO:0002641 ! has intracellular endoparasite + +[Typedef] +id: RO:0002641 +name: has intracellular endoparasite +def: "inverse of intracellular endoparasite of" [] +subset: RO:0002259 +is_a: RO:0002635 ! has endoparasite + +[Typedef] +id: RO:0008501 +name: epiphyte of +def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string +is_a: RO:0002440 ! symbiotically interacts with +inverse_of: RO:0008502 ! has epiphyte + +[Typedef] +id: RO:0008502 +name: has epiphyte +def: "inverse of epiphyte of" [] +subset: RO:0002259 +is_a: RO:0002440 ! symbiotically interacts with + +[Typedef] +id: RO:0008503 +name: kleptoparasite of +def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string +is_a: RO:0002444 ! parasite of +inverse_of: RO:0008504 ! kleptoparasitized by + +[Typedef] +id: RO:0008504 +name: kleptoparasitized by +def: "inverse of kleptoparasite of" [] +subset: RO:0002259 +is_a: RO:0002445 ! parasitized by + +[Typedef] +id: RO:0008507 +name: lays eggs on +def: "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." [] +is_a: RO:0002618 ! visits +inverse_of: RO:0008508 ! has eggs laid on by + +[Typedef] +id: RO:0008508 +name: has eggs laid on by +def: "inverse of lays eggs on" [] +is_a: RO:0002619 ! visited by + diff --git a/subsets/ro-biotic-interaction.owl b/subsets/ro-biotic-interaction.owl index 76d94dfd..9017b92f 100644 --- a/subsets/ro-biotic-interaction.owl +++ b/subsets/ro-biotic-interaction.owl @@ -65,21 +65,15 @@ - + - + - + - - - - - - - + @@ -183,7 +177,7 @@ An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level biotically interacts with @@ -198,7 +192,7 @@ An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall + trophically interacts with @@ -214,9 +208,9 @@ A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - Chris Mungall - Jorrit Poelen - Katja Shulz + + + is subject of predation interaction with preys upon @@ -233,10 +227,9 @@ A biotic interaction in which the two organisms live together in more or less intimate association. - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - symbiotically interacts with @@ -248,9 +241,8 @@ An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 - commensually interacts with @@ -262,9 +254,8 @@ An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 - mutualistically interacts with @@ -276,10 +267,9 @@ An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - Chris Mungall + http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by - interacts with via parasite-host interaction @@ -293,9 +283,8 @@ Pediculus humanus capitis parasite of human - Chris Mungall + parasitizes - direct parasite of parasite of @@ -309,7 +298,7 @@ - Chris Mungall + has parasite parasitised by directly parasitized by @@ -326,7 +315,7 @@ Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - Chris Mungall + semibiotically interacts with participates in a abiotic-biotic interaction with @@ -339,8 +328,7 @@ - - Chris Mungall + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) host of @@ -352,8 +340,8 @@ - - Chris Mungall + X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y + has host http://eol.org/schema/terms/hasHost @@ -368,7 +356,7 @@ Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - Chris Mungall + is subject of pollination interaction with pollinates @@ -381,7 +369,7 @@ - Chris Mungall + has polinator is target of pollination interaction with @@ -396,7 +384,7 @@ - Chris Mungall + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. acquires nutrients from @@ -409,7 +397,7 @@ inverse of preys on - Chris Mungall + has predator is target of predation interaction with @@ -427,7 +415,7 @@ Anopheles is a vector for Plasmodium - Chris Mungall + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism is vector for @@ -439,7 +427,7 @@ - Chris Mungall + has vector @@ -450,7 +438,7 @@ - Chris Mungall + provides nutrients for @@ -461,7 +449,7 @@ - Chris Mungall + is subject of eating interaction with eats @@ -473,7 +461,7 @@ - Chris Mungall + eaten by is target of eating interaction with @@ -493,11 +481,11 @@ x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - Chris Mungall + http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite + hyperparasitoid of epiparasite of - hyperparasitoid of hyperparasite of @@ -513,7 +501,7 @@ inverse of hyperparasite of - Chris Mungall + has epiparasite has hyperparasite hyperparasitoidized by @@ -528,7 +516,7 @@ - Chris Mungall + http://en.wikipedia.org/wiki/Allelopathy allelopath of @@ -543,7 +531,7 @@ - Chris Mungall + pathogen of @@ -554,7 +542,7 @@ - Chris Mungall + has pathogen @@ -565,7 +553,7 @@ - Chris Mungall + participates in a biotic-biotic interaction with @@ -576,7 +564,6 @@ - visits @@ -588,7 +575,6 @@ - visited by @@ -829,12 +815,12 @@ - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. + inverse of lays eggs on has eggs laid on by - + diff --git a/subsets/ro-biotic-interaction.tsv b/subsets/ro-biotic-interaction.tsv new file mode 100644 index 00000000..e69de29b diff --git a/subsets/ro-causal.json b/subsets/ro-causal.json new file mode 100644 index 00000000..7e8d7fb2 --- /dev/null +++ b/subsets/ro-causal.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-causal.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_2D_boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_2D_boundary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "lbl" : "electrically_synapsed_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions." + }, + "xrefs" : [ { + "val" : "RO:0002003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "electrically_synapsed_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002007" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "lbl" : "coincident with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." + }, + "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002008" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note from NCEAS meeting: consider changing primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "coincident_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "lbl" : "regulates in other organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "xrefs" : [ { + "val" : "RO:0002010" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_in_other_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "lbl" : "occurrent part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A part of relation that applies only between occurrents." + }, + "xrefs" : [ { + "val" : "RO:0002012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurrent_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." + }, + "xrefs" : [ { + "val" : "RO:0002013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "xrefs" : [ { + "val" : "RO:0002014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_negative_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], + "xrefs" : [ { + "val" : "RO:0002015" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_positive_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "lbl" : "has necessary component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], + "xrefs" : [ { + "val" : "RO:0002016" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_necessary_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], + "xrefs" : [ { + "val" : "RO:0002017" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:44:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "xrefs" : [ { + "val" : "RO:0002018" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "lbl" : "has ligand", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." + }, + "xrefs" : [ { + "val" : "RO:0002019" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-19T17:30:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ligand" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "lbl" : "transports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." + }, + "xrefs" : [ { + "val" : "RO:0002020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:11:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." + }, + "xrefs" : [ { + "val" : "RO:0002021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "xrefs" : [ { + "val" : "RO:0002022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:38Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. 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No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." + }, + "xrefs" : [ { + "val" : "RO:0002104" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : 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"synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002106" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that 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it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002113" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "synapses in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_presynaptic_terminal_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002114", + "lbl" : "synapsed_via_type_III_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." + }, + "comments" : [ "Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002114" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_via_type_III_bouton_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002115", + "lbl" 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 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}, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002297" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002298" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_morphogenesis_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_maturation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002300" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_disappearance_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002301" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_regression_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002302" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_treated_by_substance" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002303" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_habitat" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002304" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002305" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002309" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stimulus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002313" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports_or_maintains_localization_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "xrefs" : [ { + "val" : "RO:0002314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : 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"http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_acquisition_of_features_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002321" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "colocalizes_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002326" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002327" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enables" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "xrefs" : [ { + "val" : "RO:0002328" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "functionally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "xrefs" : [ { + "val" : "RO:0002329" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_structure_that_is_capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "xrefs" : [ { + "val" : "RO:0002331" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "xrefs" : [ { + "val" : "RO:0002332" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_levels_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002333" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enabled_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002334" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002335" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002336" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "xrefs" : [ { + "val" : "RO:0002337" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_localization_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002338" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002339" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002340" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "imports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "xrefs" : [ { + "val" : "RO:0002341" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_along" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002342" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002343" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_growth_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002344" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' 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"http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "exports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002348", + "lbl" : "results in commitment to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002348" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. 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It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. 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"RO:0002445" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitized_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. 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We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "subject_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002463" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "target_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002469" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_nutrients_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002470" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "eats" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002471" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_eaten_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002473" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "composed_primarily_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "xrefs" : [ { + "val" : "RO:0002476" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/subsets/ro-causal.obo b/subsets/ro-causal.obo index 9472403f..87ecf23c 100644 --- a/subsets/ro-causal.obo +++ b/subsets/ro-causal.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-causal -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/subsets/ro-causal.owl b/subsets/ro-causal.owl index d6ac9788..bada75b7 100644 --- a/subsets/ro-causal.owl +++ b/subsets/ro-causal.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-causal.tsv b/subsets/ro-causal.tsv new file mode 100644 index 00000000..23e4cd33 --- /dev/null +++ b/subsets/ro-causal.tsv @@ -0,0 +1,51 @@ +?x ?label +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid1 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid18 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid22 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid26 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid33 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid37 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid40 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid5 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid52 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid58 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid61 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid64 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid67 +_:B61bb9a03X2D7dfeX2D46e6X2Dabe2X2Df8ae2f677ec5genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-chado.json b/subsets/ro-chado.json new file mode 100644 index 00000000..ed2616ac --- /dev/null +++ b/subsets/ro-chado.json @@ -0,0 +1,16507 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-chado.owl", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2002/07/owl#versionInfo", + "val" : "2023-02-19" + } ], + "version" : "http://purl.obolibrary.org/obo/ro/releases/2023-02-19/subsets/ro-chado.owl" + }, + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000054", + "lbl" : "realized in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease is realized in this disease course" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is realized in this shattering" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is realized in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is realized by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "realized_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000055", + "lbl" : "realizes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "realizes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this disease course realizes this disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation realizes this investigator role" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this shattering realizes this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/iao.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000060", + "lbl" : "obsolete preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "accidentally included in BFO 1.2 proposal\n - should have been BFO_0000062" ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "occurs in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "occurs_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "unfolds_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "site of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", + "val" : "http://purl.obolibrary.org/obo/bfo.owl" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/ENVO_01003004", + "lbl" : "derives from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000078", + "lbl" : "curation status specification", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000225", + "lbl" : "obsolescence reason specification", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000426", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000589", + "lbl" : "OBO foundry unique label", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002105", + "lbl" : "synapsed_via_type_Ib_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton." + }, + "comments" : [ "Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002106", + "lbl" : "synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002107", + "lbl" : "synapsed_via_type_II_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and 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"http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "lbl" : "derived by descent from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral_stucture_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "evolutionarily_descended_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "lbl" : "has derived by descendant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of derived by descent from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "lbl" : "serially homologous to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + }, + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9227-417X" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002171", + "lbl" : "mutually spatially disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "non-overlapping with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no parts with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX owl: \nPREFIX part_of: \nPREFIX mutually_spatially_disjoint_with: \nCONSTRUCT {\n part_of: a owl:ObjectProperty .\n [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?x ;\n owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?y\n ]\n ]\n}\nWHERE {\n ?x mutually_spatially_disjoint_with: ?y .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/RO_0002163" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002172", + "lbl" : "taxonomic class assertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002173", + "lbl" : "ambiguous for taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002174", + "lbl" : "dubious for taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T." + }, + "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" + }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002204", + "lbl" : "gene product of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "lbl" : "has gene product", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002214", + "lbl" : "has prototype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002217", + "lbl" : "obsolete actively participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" + }, + "comments" : [ "Obsoleted as the inverse property was obsoleted." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "agent in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002608" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002218", + "lbl" : "obsolete has active participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has agent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002500" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Allen" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ends with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "finished by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002245", + "lbl" : "over-expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002246", + "lbl" : "under-expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "lbl" : "defined by inverse", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002291", + "lbl" : "ubiquitously expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'expressed in'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002293", + "lbl" : "ubiquitously expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ubiquiotously expressed in" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002312", + "lbl" : "evolutionary variant of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002345", + "lbl" : "exports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002348", + "lbl" : "results in commitment to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002349", + "lbl" : "results in determination of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "lbl" : "member of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "is member of is a mereological relation between a item and a collection." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An organism that is a member of a population of organisms" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is member of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "member part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "lbl" : "has member", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "SIO" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "lbl" : "input of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has input" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "lbl" : "output of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has output" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "lbl" : "formed as result of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002355", + "lbl" : "results in structural organization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002356", + "lbl" : "results in specification of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002374", + "lbl" : "derived from ancestral fusion of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" + }, + "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "has fused element" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002401", + "lbl" : "obsolete has indirect input", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002402", + "lbl" : "obsolete has direct output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "translation SubClassOf has_direct_output some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly produces" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002403", + "lbl" : "obsolete has indirect output", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002406", + "lbl" : "obsolete directly activates", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002629" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002408", + "lbl" : "obsolete directly inhibits", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002630" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002416", + "lbl" : "logical macro assertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002419", + "lbl" : "annotation property cardinality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002420", + "lbl" : "logical macro assertion on a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a class" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002421", + "lbl" : "logical macro assertion on a property", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a property" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002422", + "lbl" : "logical macro assertion on an object property", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "lbl" : "logical macro assertion on an annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002424", + "lbl" : "differs in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This is an exploratory relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002425", + "lbl" : "differs in attribute of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "lbl" : "differs in attribute", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000316" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0208" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "lbl" : "molecularly interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "binds" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "molecularly binds with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0915" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002437", + "lbl" : "biotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "interacts with on organism level" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/interactsWith" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002438", + "lbl" : "trophically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the partners are related via a feeding relationship." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "lbl" : "preys on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Baleen whale preys on krill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7134-3324" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of predation interaction with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preys upon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/preysUpon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.inaturalist.org/observations/2942824" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002440", + "lbl" : "symbiotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction in which the two organisms live together in more or less intimate association." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002441", + "lbl" : "commensually interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002442", + "lbl" : "mutualistically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "lbl" : "interacts with via parasite-host interaction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002444", + "lbl" : "parasite of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "direct parasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Pediculus humanus capitis parasite of human" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitizes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/parasitizes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002445", + "lbl" : "parasitized by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "directly parasitized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "semibiotically interacts with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Porifiera attaches to substrate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002447", + "lbl" : "phosphorylates", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "lbl" : "directly regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly decreases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly inhibits" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "lbl" : "directly positively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly increases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly activates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002451", + "lbl" : "transmitted by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a disease and organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "all dengue disease transmitted by some mosquito" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Add domain and range constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002452", + "lbl" : "has symptom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between a disease or an organism and a phenotype" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002453", + "lbl" : "host of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "lbl" : "has host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasHost" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002455", + "lbl" : "pollinates", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Bees pollinate Flowers" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/pollinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "lbl" : "pollinated by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has polinator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasPollinator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "lbl" : "acquires nutrients from", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002458", + "lbl" : "preyed upon by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of preys on" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has predator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of predation interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/HasPredator" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "lbl" : "is vector for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002460", + "lbl" : "has vector", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002461", + "lbl" : "partner in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002462", + "lbl" : "subject participant in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002464", + "lbl" : "helper property (not for use in curation)", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002465", + "lbl" : "is symbiosis", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002466", + "lbl" : "is commensalism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002467", + "lbl" : "is mutualism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002468", + "lbl" : "is parasitism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002472", + "lbl" : "is evidence for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002474", + "lbl" : "dispositional interpretation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002475", + "lbl" : "has no connections with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no connection with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002481", + "lbl" : "is kinase activity", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002482", + "lbl" : "is ubiquitination", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002483", + "lbl" : "inherited annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002484", + "lbl" : "curator guidance link", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "exists during" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/BFO_0000169" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002503", + "lbl" : "towards", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002504", + "lbl" : "always present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brain always_present_in_taxon 'Vertebrata'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "forelimb always_present_in_taxon Euarchontoglires" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "never lost in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002505", + "lbl" : "has intermediate", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has intermediate product" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002506", + "lbl" : "causal relation between entities", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002507", + "lbl" : "determined by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A coral reef environment is determined by a particular coral reef" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/24330602" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determined by (system to material entity)" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002508", + "lbl" : "determines", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of determined by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determines (material entity to system)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002509", + "lbl" : "determined by part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002510", + "lbl" : "transcribed from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is transcribed from y if and only if x is synthesized from template y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002511", + "lbl" : "transcribed to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of transcribed from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002512", + "lbl" : "ribosomal translation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002513", + "lbl" : "ribosomally translates to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ribosomal translation of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002514", + "lbl" : "sequentially related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are sequentially adjacent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002516", + "lbl" : "has start sequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002518", + "lbl" : "has end sequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ended by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002519", + "lbl" : "is end sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has end sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002520", + "lbl" : "is consecutive sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the SO paper, this was defined as an instance-type relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002521", + "lbl" : "is sequentially aligned with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "lbl" : "bounds sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002523", + "lbl" : "is bound by sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of bounds sequence of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "lbl" : "has subsequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contains" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "lbl" : "is subsequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has subsequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained by" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "lbl" : "overlaps sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002527", + "lbl" : "does not overlap sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "disconnected from" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "lbl" : "is upstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of downstream of sequence of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "lbl" : "is downstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002530", + "lbl" : "is immediately downstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002529" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002531", + "lbl" : "is immediately upstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of immediately downstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002535", + "lbl" : "temporal logical macro assertion on a class", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002536", + "lbl" : "measurement property has unit", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002537", + "lbl" : "has start time value", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002538", + "lbl" : "has end time value", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002539", + "lbl" : "start, days post fertilization", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002540", + "lbl" : "end, days post fertilization", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002541", + "lbl" : "start, years post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002542", + "lbl" : "end, years post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002543", + "lbl" : "start, months post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002544", + "lbl" : "end, months post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002545", + "lbl" : "month of gestation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002546", + "lbl" : "has developmental stage marker", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002547", + "lbl" : "start, days post coitum", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of coitum." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002548", + "lbl" : "end, days post coitum", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the end of the stage and the time of coitum." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002549", + "lbl" : "start, weeks post birth", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002550", + "lbl" : "end, weeks post birth", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002551", + "lbl" : "has skeleton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has supporting framework" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002552", + "lbl" : "results in ending of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002553", + "lbl" : "hyperparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "hyperparasitoid of" + }, { + "pred" : "hasRelatedSynonym", + "val" : "epiparasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://eol.org/schema/terms/hyperparasitoidOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Hyperparasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "lbl" : "hyperparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of hyperparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "has epiparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has hyperparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hyperparasitoidized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002555", + "lbl" : "allelopath of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Allelopathy" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/allelopathyYes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002556", + "lbl" : "pathogen of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002557", + "lbl" : "has pathogen", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002558", + "lbl" : "has evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of is evidence for" + }, + "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/25052702" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "lbl" : "causally influenced by", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influenced by (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002560", + "lbl" : "is asymmetric relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002561", + "lbl" : "is symmetric relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002562", + "lbl" : "is relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "lbl" : "interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "lbl" : "molecular interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002565", + "lbl" : "results in movement of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "lbl" : "causally influences", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "lbl" : "biomechanically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002568", + "lbl" : "has muscle antagonist", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Antagonist_(muscle)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002569", + "lbl" : "has branching part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of branching part of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "lbl" : "conduit for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "UBERON:cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002571", + "lbl" : "lumen of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:cjm" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002572", + "lbl" : "luminal space of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002573", + "lbl" : "has modifier", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between an attribute or a qualifier and another attribute." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002574", + "lbl" : "participates in a biotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002575", + "lbl" : "is direct form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002423", + "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "lbl" : "skeleton of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has skeleton" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "lbl" : "directly regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002579", + "lbl" : "is indirect form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002580", + "lbl" : "logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002581", + "lbl" : "is a defining property chain axiom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002583", + "lbl" : "existence starts at end of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002584", + "lbl" : "has part structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002585", + "lbl" : "results in closure of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002586", + "lbl" : "results in breakdown of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002587", + "lbl" : "results in synthesis of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002588", + "lbl" : "results in assembly of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002589", + "lbl" : "results in catabolism of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002590", + "lbl" : "results in disassembly of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002591", + "lbl" : "results in remodeling of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002592", + "lbl" : "results in organization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002593", + "lbl" : "existence ends at start of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002594", + "lbl" : "is relational form of a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "lbl" : "causal relation between material entity and a process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002596", + "lbl" : "capable of regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pyrethroid -> growth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "lbl" : "capable of negatively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "lbl" : "capable of positively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "renin -> arteriolar smooth muscle contraction" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002599", + "lbl" : "capable of inhibiting or preventing pathological process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pazopanib -> pathological angiogenesis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002600", + "lbl" : "capable of upregulating or causing pathological process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "benzene -> cancer [CHEBI]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "causes disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002601", + "lbl" : "logical macro assertion involving identity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A shortcut relationship that holds between two entities based on their identity criteria" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002602", + "lbl" : "in approximate one to one relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002603", + "lbl" : "is approximately equivalent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002604", + "lbl" : "is opposite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002605", + "lbl" : "is indistinguishable from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002606", + "lbl" : "is substance that treats", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002607", + "lbl" : "is marker for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be ceded to OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002608", + "lbl" : "process has causal agent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'causal agent in process'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002609", + "lbl" : "obsolete related via dependence to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002610", + "lbl" : "correlated with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Groups both positive and negative correlation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002611", + "lbl" : "evidential logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002612", + "lbl" : "axiom has evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002613", + "lbl" : "axiom contradicted by evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002614", + "lbl" : "is evidence with support from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." + }, + "comments" : [ "In the Gene Ontology association model, this corresponds to the With/From field" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002615", + "lbl" : "has model", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of is-model-of" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002616", + "lbl" : "related via evidence or inference to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002617", + "lbl" : "is representative IRI for equivalence set", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002618", + "lbl" : "visits", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/74" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002619", + "lbl" : "visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002622", + "lbl" : "visits flowers of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002623", + "lbl" : "has flowers visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002624", + "lbl" : "lays eggs in", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002625", + "lbl" : "has eggs laid in by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002626", + "lbl" : "kills", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://github.com/jhpoelen/eol-globi-data/issues/143" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002627", + "lbl" : "is killed by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "lbl" : "directly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002630", + "lbl" : "directly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002632", + "lbl" : "ectoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002633", + "lbl" : "has ectoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ectoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002634", + "lbl" : "endoparasite of", + "type" : "PROPERTY", + "meta" : { + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "lives inside of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002635", + "lbl" : "has endoparasite", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002636", + "lbl" : "mesoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002637", + "lbl" : "has mesoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of mesoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002638", + "lbl" : "intercellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002639", + "lbl" : "has intercellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intercellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002640", + "lbl" : "intracellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002641", + "lbl" : "has intracellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intracellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002801", + "lbl" : "co-roosts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Communal_roosting" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003000", + "lbl" : "produces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." + }, + "comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "lbl" : "produced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a produced_by b iff some process that occurs_in b has_output a." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003002", + "lbl" : "represses expression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003003", + "lbl" : "increases expression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "lbl" : "has role in modeling", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." + }, + "comments" : [ "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-1048-5019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is used to study" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "lbl" : "causes or contributes to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." + }, + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003303", + "lbl" : "causes condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "lbl" : "contributes to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "lbl" : "contributes to severity of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to expressivity of condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003306", + "lbl" : "contributes to frequency of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to penetrance of condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "lbl" : "ameliorates condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." + }, + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preventative for condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003308", + "lbl" : "correlated with condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003309", + "lbl" : "exacerbates condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003310", + "lbl" : "condition ameliorated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003311", + "lbl" : "condition exacerbated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004000", + "lbl" : "condition has genetic basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:38:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004001", + "lbl" : "has material basis in gain of function germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:20Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410295" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410296" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004002", + "lbl" : "has material basis in loss of function germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004003", + "lbl" : "has material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:54Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004004", + "lbl" : "has material basis in somatic mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:07Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004005", + "lbl" : "has major susceptibility factor", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:26Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004006", + "lbl" : "has partial material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:57Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004007", + "lbl" : "has primary input or output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004008", + "lbl" : "has primary output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", + "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004009", + "lbl" : "has primary input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", + "xrefs" : [ "GOC:cjm", "GOC:dph", "GOC:kva", "GOC:pt" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:56Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004010", + "lbl" : "is genetic basis for condition", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:53:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004011", + "lbl" : "is causal gain of function germline mutation of in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : 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"http://purl.obolibrary.org/obo/RO_0004013", + "lbl" : "is causal germline mutation in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:56:40Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004014", + "lbl" : "is causal somatic mutation in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:57:07Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004015", + "lbl" : "is causal susceptibility factor for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + 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"http://purl.obolibrary.org/obo/RO_0004017", + "lbl" : "realizable has basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:01Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004018", + "lbl" : "is basis for realizable", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004019", + "lbl" : "disease has basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:26:47Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004020", + "lbl" : "disease has basis in dysfunction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in dysfunction of (disease to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:29:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004021", + "lbl" : "disease has basis in disruption of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:37:52Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004022", + "lbl" : "disease has basis in feature", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the 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It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:50:54Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004024", + "lbl" : "disease causes disruption of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:51:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004025", + "lbl" : "disease causes dysfunction of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes dysfunction of (disease to anatomical entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:58:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004026", + "lbl" : "disease has location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T04:06:02Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004027", + "lbl" : "disease has inflammation site", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:37:31Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004029", + "lbl" : "disease has feature", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:50:53Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "lbl" : "disease arises from alteration in structure", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "lbl" : "enables subfunction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-25T23:20:13Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "lbl" : "acts upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:30Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "lbl" : "acts upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:51Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "lbl" : "acts upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "lbl" : "acts upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004036", + "lbl" : "nominally disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004048", + "lbl" : "is directional form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:59:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004049", + "lbl" : "is positive form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:16Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004096", + "lbl" : "DEPRECATED inheres in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information." ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004097", + "lbl" : "DEPRECATED bearer of", + "type" : "PROPERTY", + "meta" : { + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007000", + "lbl" : "has driver", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007001", + "lbl" : "has disease driver", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008501", + "lbl" : "epiphyte of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Epiphyte" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008502", + "lbl" : "has epiphyte", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of epiphyte of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008503", + "lbl" : "kleptoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008504", + "lbl" : "kleptoparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of kleptoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008505", + "lbl" : "creates habitat for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008506", + "lbl" : "ecologically co-occurs with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008507", + "lbl" : "lays eggs on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008508", + "lbl" : "has eggs laid on by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of lays eggs on" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009001", + "lbl" : "has substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "muffin 'has substance added' some 'baking soda'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009002", + "lbl" : "has substance removed", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'egg white' 'has substance removed' some 'egg yolk'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009003", + "lbl" : "immersed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardines 'immersed in' some 'oil and mustard'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009004", + "lbl" : "has consumer", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardine has consumer some homo sapiens" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009005", + "lbl" : "has primary substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bread 'has primary substance added' some 'flour'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "lbl" : "realized in response to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "triggered by process", + "xrefs" : [ "RO:cjm" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : 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"receives synaptic input throughout", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:55:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013006", + "lbl" : "sends synaptic output throughout", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:57:27Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013007", + "lbl" : "has sensory dendrite in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has sensory dendrite location" + }, { + "pred" : "hasExactSynonym", + "val" : "has sensory terminal in" + }, { + "pred" : "hasExactSynonym", + "val" : "has sensory terminal location" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-20T12:10:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013008", + "lbl" : "receives synaptic input from neuron", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-05-26T08:40:18Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013009", + "lbl" : "sends synaptic output to cell", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." + }, + "comments" : [ "Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-05-26T08:41:07Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0014001", + "lbl" : "disease has infectious agent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015001", + "lbl" : "has exemplar data", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-5260-9315" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is not meant to capture the relation between occurrents and data." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015002", + "lbl" : "exemplar data of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-5260-9315" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015003", + "lbl" : "subcluster of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a group and another group it is part of but does not fully constitute." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7258-9596" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context." + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015006", + "lbl" : "different in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015007", + "lbl" : "increased in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "lbl" : "decreased in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015009", + "lbl" : "similar in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "lbl" : "has relative magnitude", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015011", + "lbl" : "has cross section", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015012", + "lbl" : "reciprocal of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015015", + "lbl" : "has high plasma membrane amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "lbl" : "has low plasma membrane amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016001", + "lbl" : "has phenotype or disease", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016002", + "lbl" : "has disease", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:44Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016004", + "lbl" : "has exposure medium", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000083" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-12-14T20:41:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7463-6306" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017001", + "lbl" : "device utilizes material", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "utilizes" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A diagnostic testing device utilizes a specimen." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-2620-0345" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-11-08T12:00:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018001", + "lbl" : "is myristoyltransferase activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Helper relation for OWL definition of RO:0018002 myristoylates" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018002", + "lbl" : "myristoylates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/conformsTo", + "val" : "http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018003", + "lbl" : "myristoylated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of myristoylates" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018027", + "lbl" : "is agonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P3772" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018028", + "lbl" : "is inverse agonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + 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"http://purl.obolibrary.org/obo/RO_0002339", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002380", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002377", "http://purl.obolibrary.org/obo/RO_0002381" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002413", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002402", "http://purl.obolibrary.org/obo/RO_0002400" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002409" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002403", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002402" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002553", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002444", "http://purl.obolibrary.org/obo/RO_0002444" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002554", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002445", "http://purl.obolibrary.org/obo/RO_0002445" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000062" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/RO_0002082" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000063" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002509", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002507", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002205", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002511", "http://purl.obolibrary.org/obo/RO_0002513" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002204", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002512", "http://purl.obolibrary.org/obo/RO_0002510" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002526", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002524", "http://purl.obolibrary.org/obo/RO_0002525" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002583", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002593", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004024", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013002", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013003", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013003", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013007", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0015001", "http://purl.obolibrary.org/obo/RO_0015003" ] + } ] + } ] +} \ No newline at end of file diff --git a/subsets/ro-chado.obo b/subsets/ro-chado.obo index 300fa699..6dedea73 100644 --- a/subsets/ro-chado.obo +++ b/subsets/ro-chado.obo @@ -5,21 +5,6 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 60 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 7] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 49 Logical Axioms: 12] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 9 Logical Axioms: 3] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 310 Logical Axioms: 68] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 6 Logical Axioms: 2] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 18 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 0 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 45 Logical Axioms: 10] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 29 Logical Axioms: 9] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 3 Logical Axioms: 0] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 104 Logical Axioms: 26] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 20 Logical Axioms: 6] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 731 Logical Axioms: 148] -remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 146 Logical Axioms: 45] default-namespace: relationship ontology: ro/subsets/ro-chado.obo property_value: http://purl.org/dc/elements/1.1/description "The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies." xsd:string @@ -91,6 +76,11 @@ id: BFO:0000067 name: contains_process def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +[Typedef] +id: ENVO:01003004 +name: derives_from_part_of +def: "A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity." [] + [Typedef] id: RO:0000052 name: characteristic_of diff --git a/subsets/ro-chado.owl b/subsets/ro-chado.owl new file mode 100644 index 00000000..23ffa7b2 --- /dev/null +++ b/subsets/ro-chado.owl @@ -0,0 +1,12379 @@ + + + + + 2023-02-19 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. + + + + + + + + + + OBO foundry unique label + + + + + + + + + + + + + + + + + + + + + term replaced by + + + + + + + + 'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + } + Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. + + + defined by construct + + + + + + + + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + temporal interpretation + + + + + + + + + + tooth SubClassOf 'never in taxon' value 'Aves' + x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. + + + + Class: ?X DisjointWith: RO_0002162 some ?Y + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> +PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> +CONSTRUCT { + in_taxon: a owl:ObjectProperty . + ?x owl:disjointWith [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom ?taxon + ] . + ?x rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom [ + a owl:Class ; + owl:complementOf ?taxon + ] + ] . +} +WHERE { + ?x never_in_taxon: ?taxon . +} + never in taxon + + + + + + + + + + A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. + non-overlapping with + shares no parts with + + Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) + PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> +PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> +CONSTRUCT { + part_of: a owl:ObjectProperty . + [ + a owl:Restriction ; + owl:onProperty part_of: ; + owl:someValuesFrom ?x ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty part_of: ; + owl:someValuesFrom ?y + ] + ] +} +WHERE { + ?x mutually_spatially_disjoint_with: ?y . +} + mutually spatially disjoint with + + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + + + + + + + + + An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. + taxonomic class assertion + + + + + + + + + + S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] + ambiguous for taxon + + + + + + + + + + S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. + + + This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost + dubious for taxon + + + + + + + + + + S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S + + + PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> +PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> +CONSTRUCT { + in_taxon: a owl:ObjectProperty . + ?witness rdfs:label ?label . + ?witness rdfs:subClassOf ?x . + ?witness rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty in_taxon: ; + owl:someValuesFrom ?taxon + ] . +} +WHERE { + ?x present_in_taxon: ?taxon . + BIND(IRI(CONCAT( + "http://purl.obolibrary.org/obo/RO_0002175#", + MD5(STR(?x)), + "-", + MD5(STR(?taxon)) + )) as ?witness) + BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) +} + The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. + present in taxon + + + + + + + + + + defined by inverse + + + + + + + + + An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. + logical macro assertion + http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ + + + + + + + + An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. + annotation property cardinality + + + + + + + + + + A logical macro assertion whose domain is an IRI for a class + The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL + logical macro assertion on a class + + + + + + + + + A logical macro assertion whose domain is an IRI for a property + logical macro assertion on a property + + + + + + + + + Used to annotate object properties to describe a logical meta-property or characteristic of the object property. + logical macro assertion on an object property + + + + + + + + + logical macro assertion on an annotation property + + + + + + + + + An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. + dispositional interpretation + + + + + + + + + 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' + A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. + shares no connection with + Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) + has no connections with + + + + + + + + + inherited annotation property + + + + + + + + Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) + curator guidance link + + + + + + + + + brain always_present_in_taxon 'Vertebrata' + forelimb always_present_in_taxon Euarchontoglires + S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S + This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. + never lost in + always present in taxon + + + + + + + + + This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. + temporal logical macro assertion on a class + + + + + + + + + measurement property has unit + + + + + + + + + has start time value + + + + + + + + + + has end time value + + + + + + + + + + Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. + start, days post fertilization + + + + + + + + + + Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. + end, days post fertilization + + + + + + + + + + Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. + start, years post birth + + + + + + + + + + Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 + end, years post birth + + + + + + + + + + Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. + start, months post birth + + + + + + + + + + Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 + end, months post birth + + + + + + + + + + Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. + month of gestation + + + + + + + + + + A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process + has developmental stage marker + + + + + + + + + + Count of number of days intervening between the start of the stage and the time of coitum. + For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) + start, days post coitum + + + + + + + + + + Count of number of days intervening between the end of the stage and the time of coitum. + end, days post coitum + + + + + + + + + + start, weeks post birth + + + + + + + + + + end, weeks post birth + + + + + + + + + + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p + is asymmetric relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p + is symmetric relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process + is relational form of process class + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y + The general property hierarchy is: + + "directly P" SubPropertyOf "P" + Transitive(P) + +Where we have an annotation assertion + + "directly P" "is direct form of" "P" + If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' + + is direct form of + + + + + + + + + + relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y + + is indirect form of + + + + + + + + + + logical macro assertion on an axiom + + + + + + + + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom + + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. + is relational form of a class + + + + + + + + + A shortcut relationship that holds between two entities based on their identity criteria + logical macro assertion involving identity + + + + + + + + + A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. + in approximate one to one relationship with + + + + + + + + + x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y + The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" + is approximately equivalent to + + + + + + + + + 'anterior end of organism' is-opposite-of 'posterior end of organism' + 'increase in temperature' is-opposite-of 'decrease in temperature' + x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + is opposite of + + + + + + + + + x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). + is indistinguishable from + + + + + + + + + evidential logical macro assertion on an axiom + + + + + + + + + A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom has evidence + + + + + + + + + A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom + This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. + axiom contradicted by evidence + + + + + + + + + In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. + this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. + If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion + is representative IRI for equivalence set + OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member + + + + + + + + + true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. + + nominally disjoint with + + + + + + + + + Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" + + 2018-03-13T23:59:29Z + is directional form of + + + + + + + + + + 2018-03-14T00:03:16Z + is positive form of + + + + + + + + + + 2018-03-14T00:03:24Z + is negative form of + + + + + + + + + part-of is homeomorphic for independent continuants. + R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. + + 2018-10-21T19:46:34Z + R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. + is homeomorphic for + + + + + + + + + + pg + 2020-09-22T11:05:29Z + valid_for_go_annotation_extension + + + + + + + + + + pg + 2020-09-22T11:05:18Z + valid_for_go_gp2term + + + + + + + + + + pg + 2020-09-22T11:04:12Z + valid_for_go_ontology + + + + + + + + + + pg + 2020-09-22T11:05:45Z + valid_for_gocam + + + + + + + + + + eco subset + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subset_property + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_broad_synonym + + + + + + + + database_cross_reference + + + + + + + + has_exact_synonym + + + + + + + + has_narrow_synonym + + + + + + + + has_obo_format_version + + + + + + + + has_related_synonym + + + + + + + + + + + + + + in_subset + + + + + + + + + + + + + + + + + + + + is defined by + + + + + is defined by + This is an experimental annotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + + + + + + + + + + + + part of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + + + + has part + + + + + + + + + realized in + this disease is realized in this disease course + this fragility is realized in this shattering + this investigator role is realized in this investigation + is realized by + realized_in + [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + + + + + + + + realizes + this disease course realizes this disease + this investigation realizes this investigator role + this shattering realizes this fragility + to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + + + + + + + + + accidentally included in BFO 1.2 proposal + - should have been BFO_0000062 + obsolete preceded by + true + + + + + + + + + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by + + + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in + + + + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity. + derives from part of + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + has characteristic + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + inverse of has disposition + + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + + + + + + + + + + OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete in neural circuit with + true + + + + + + + + + + OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete upstream in neural circuit with + true + + + + + + + + + + OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. + + + + Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). + obsolete downstream in neural circuit with + true + + + + + + + + + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. + + derives from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + + derives into + + + + + + + + + + is location of + my head is the location of my brain + this cage is the location of this rat + a relation between two independent continuants, the location and the target, in which the target is entirely within the location + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + location_of + + location of + + + + + + + + + + + + + contained in + Containment is location not involving parthood, and arises only where some immaterial continuant is involved. + Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): + Intended meaning: +domain: material entity +range: spatial region or site (immaterial continuant) + + contained_in + + + contained in + + + + + + + + contains + + + contains + + + + + + + + + + penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is allergic trigger for + + + + + + + + + + A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + is autoimmune trigger for + + + + + + + + + penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has allergic trigger + + + + + + + + + A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. + has autoimmune trigger + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in + + located in + + + + + + + + + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of + surface of + + 2D boundary of + + + + + + + + + + May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 + + + aligned with + + + + + + + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + + has boundary + has_2D_boundary + + has 2D boundary + + + + + + + + + A relation that holds between two neurons that are electrically coupled via gap junctions. + + + electrically_synapsed_to + + + + + + + + + The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). + + tracheates + + + + + + + + + + http://www.ncbi.nlm.nih.gov/pubmed/22402613 + innervated_by + + + + + + + + + + + + has synaptic terminal of + + + + + + + + + X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. + bounding layer of + + + + + + + + + A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. + Note from NCEAS meeting: consider changing primary label + + + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. + coincident with + + + + + + + + + A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. + + x 'cell expresses' y iff: +cell(x) +AND gene(y) +AND exists some 'transcription, DNA templated (GO_0006351)'(t) +AND t occurs_in x +AND t has_input y + cell expresses + + + + + + + + + x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). + + regulates in other organism + + + + + + + + + + + + A relationship that holds between a process that regulates a transport process and the entity transported by that process. + + + regulates transport of + + + + + + + + + + A part of relation that applies only between occurrents. + occurrent part of + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + + dos + 2017-05-24T09:36:08Z + A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. + has necessary component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + dos + 2017-07-19T17:30:36Z + has ligand + + + + + + + + + Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. + dos + 2017-07-20T17:11:08Z + transports + + + + + + + + + A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. + dos + 2017-07-20T17:19:37Z + occurs across + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + A relationship that holds between two images, A and B, where: +A depicts X; +B depicts Y; +X and Y are both of type T' +C is a 2 layer image consiting of layers A and B; +A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. +Note: A and B may be 2D or 3D. +Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. + dos + 2017-12-07T12:58:06Z + in register with + + + + + A relationship that holds between two images, A and B, where: +A depicts X; +B depicts Y; +X and Y are both of type T' +C is a 2 layer image consiting of layers A and B; +A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. +Note: A and B may be 2D or 3D. +Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. + GOC:dos + + + + + + + + + David Osumi-Sutherland + <= + + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + + + + + David Osumi-Sutherland + + starts before + + + + + + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + David Osumi-Sutherland + io + + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + + + + + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during + + + + + + + + + + + + + + Relation between a neuron and an anatomical structure that its soma is part of. + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) + + has soma location + + + + + + + + + + + relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. + + + fasciculates with + (forall (?x ?y) + (iff + (fasciculates_with ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron ; CL_0000540" ?x) + ("neuron projection bundle ; CARO_0001001" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500' " ?npbs) + (part_of ?npbs ?y) + (part_of ?nps ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + + fasciculates with + + + + + + + + + + + + + + Relation between a neuron and some structure its axon forms (chemical) synapses in. + + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( + <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) + + + axon synapses in + + + + + + + + + + + Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + synapsed by + + + + + + + + + Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] + + Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. + + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) + + has plasma membrane part + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. + + + BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_Ib_bouton_to + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. + + + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_Is_bouton_to + + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type II bouton. + + + BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_II_bouton_to + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type II bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_II_bouton + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_Ib_bouton + + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + + + synapsed in + http://purl.obolibrary.org/obo/BFO_0000051 some ( + http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( + http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) + + + has postsynaptic terminal in + + + + + + + + + has neurotransmitter + releases neurotransmitter + + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. + + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_Is_bouton + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. + synapses in + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) + + + has presynaptic terminal in + + + + + + + + + + A relation between a motor neuron and a muscle that it synapses to via a type III bouton. + BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) + + + Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) + synapsed_via_type_III_bouton_to + + + + + + + + + Relation between a muscle and a motor neuron that synapses to it via a type III bouton. + + BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) + + + Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) + synapsed_by_via_type_III_bouton + + + + + + + + + + Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + N1 synapsed_to some N2 +Expands to: +N1 SubclassOf ( + has_part some ( + ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( + ‘synapse ; GO:0045202’ that has_part some ( + ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) + synapsed to + + + + + + + + + + + + + + Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. + + + + + <http://purl.obolibrary.org/obo/BFO_0000051> some ( + <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( + http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( + <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) + + + dendrite synapsed in + + + + + + + + + + + + + + A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. + + has synapse in + <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) + + + has synaptic terminal in + + + + + + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + + + overlaps + + + + + + + + + true + + + + + + + + + + The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. + + has fasciculating component + (forall (?x ?y) + (iff + (has_fasciculating_neuron_projection ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron projection bundle ; CARO_0001001" ?x) + ("neuron projection ; GO0043005" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500" ?npbs) + (part_of ?nps ?y) + (part_of ?npbs ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + + + + + has fasciculating neuron projection + + + + + + + + + + + + + Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. +T innervates some R +Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) + + + innervates + + + + + + + + + + + X continuous_with Y if and only if X and Y share a fiat boundary. + + connected to + The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) + + continuous with + FMA:85972 + + + + + + + + + + x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x + We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom + proper overlaps + (forall (?x ?y) + (iff + (proper_overlaps ?x ?y) + (and + (overlaps ?x ?y) + (not (part_of ?x ?y)) + (not (part_of ?y ?x))))) + + + partially overlaps + + + + + + + + + + + + d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + ancestral_stucture_of + evolutionarily_descended_from + derived by descent from + + + + + + + + + + + inverse of derived by descent from + + has derived by descendant + + + + + + + + + + + + + + + + two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + Consider obsoleting and merging with child relation, 'in homology relationship with' + VBO calls this homologous_to + shares ancestor with + + + + + + + + + + + + serially homologous to + + + + + + + + + lactation SubClassOf 'only in taxon' some 'Mammalia' + + x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. + + 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria + + + + only in taxon + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + + + + + + Connects a biological entity to its taxon of origin. + in taxon + + + + + + + + + + + A is spatially_disjoint_from B if and only if they have no parts in common + There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. + + + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy + BFO_0000051 exactly 0 (BFO_0000050 some ?Y) + + + spatially disjoint from + https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern + + + + + + + + + + + + + + + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b + + connected to + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + + + + + + + + + The M8 connects Glasgow and Edinburgh + a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). + c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. + + connects + https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern + https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern + + + + + + + + + + + + + + a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. + attached to part of (anatomical structure to anatomical structure) + attached to part of + + + + + + + + + true + + + + + + + + + Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. + Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure + + supplies + + + + + + + + + Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. + Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure + + drains + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component + + + + + + + + + + + + A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). + + + has phenotype + + + + + + + + + + inverse of has phenotype + + + + phenotype of + + + + + + + + + + + + x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + + + + + This is the transitive form of the develops from relation + develops from + + + + + + + + + + + + + inverse of develops from + + + + + develops into + + + + + + + + + + + + + + + definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" + We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. + + gene product of + + + + + + + + + + + + + every HOTAIR lncRNA is the gene product of some HOXC gene + every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene + + x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y + + has gene product + + + + + + + + + + + + + + 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' + + x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process + + expressed in + + + + + + + + + + + Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. + + + FBbt + + has developmental precursor + TODO - add child relations from DOS + directly develops from + + + + + + + + + + A parasite that kills or sterilizes its host + parasitoid of + + + + + + + + + inverse of parasitoid of + + has parasitoid + + + + + + + + + + inverse of directly develops from + developmental precursor of + + directly develops into + + + + + + + + + + + + + + + + + + + + + + + p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. + + + + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + + + + regulates + + + + + + + + + + + + + + + p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. + + + negatively regulates (process to process) + + + + + negatively regulates + + + + + + + + + + + + + + + + + + + + p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. + + + positively regulates (process to process) + + + + + positively regulates + + + + + + + + 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) + heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') + + x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. + Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) + TODO: add homeomorphy axiom + This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. + + has prototype + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + + capable of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + + has function in + capable of part of + + + + + + + + + + true + + + + + + + + OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role + + agent in + + Obsoleted as the inverse property was obsoleted. + obsolete actively participates in + true + + + + + + + + OBSOLETE x has participant y if and only if x realizes some active role that inheres in y + + has agent + + obsolete has active participant + true + + + + + + + + + + + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x + + + surrounded by + + + + + + + + + A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. + The epidermis layer of a vertebrate is adjacent to the dermis. + The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. + The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. + + x adjacent to y if and only if x and y share a boundary. + This relation acts as a join point with BSPO + + + + + + adjacent to + + + + + A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. + + + + + + + + + + + inverse of surrounded by + + + + surrounds + + + + + + + + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + inverse of starts with + + Chris Mungall + Allen + + starts + + + + + + + + + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + started by + + starts with + + + + + + + + + + + + + + x develops from part of y if and only if there exists some z such that x develops from z and z is part of y + + develops from part of + + + + + + + + + + + + + + x develops_in y if x is located in y whilst x is developing + + EHDAA2 + Jonathan Bard, EHDAA2 + develops in + + + + + + + + + A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. + obligate parasite of + + + + + + + + + A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. + facultative parasite of + + + + + + + + + + + + inverse of ends with + + Chris Mungall + + ends + + + + + + + + + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + Chris Mungall + finished by + + ends with + + + + + + + + + + + + + + x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y + + starts with process that occurs in + + has start location + + + + + + + + + + + + + + x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y + + ends with process that occurs in + + has end location + + + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + consumes + + + + + has input + + + + + + + + + + + + + + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + + produces + + + + + has output + + + + + + + + + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) + stem parasite of + + + + + + + + + A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) + root parasite of + + + + + + + + + A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. + hemiparasite of + + + + + + + + + X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. + + This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). + +If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. + has component participant + + + + + + + + + A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. + ExO:0000001 + has exposure receptor + + + + + + + + + A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. + ExO:0000000 + has exposure stressor + + + + + + + + + A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor + ExO:0000055 + has exposure route + + + + + + + + + A broad relationship between an exposure event or process and the course takes from the source to the target. + http://purl.obolibrary.org/obo/ExO_0000004 + has exposure transport path + + + + + + + + + Any relationship between an exposure event or process and any other entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. + related via exposure to + + + + + + + + + g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. + over-expressed in + + + + + + + + + g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. + under-expressed in + + + + + + + + + + Any portion of roundup 'has active ingredient' some glyphosate + A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. + has active substance + has active pharmaceutical ingredient + has active ingredient + + + + + + + + + inverse of has active ingredient + + active ingredient in + + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. + b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. + + connecting branch of + + + + + + + + + + inverse of connecting branch of + + + has connecting branch + + + + + + + + + + + + + + Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] + + x has developmental contribution from y iff x has some part z such that z develops from y + + has developmental contribution from + + + + + + + + + + + + + + + inverse of has developmental contribution from + + + developmentally contributes to + + + + + + + + + + + t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T + + + + induced by + + Developmental Biology, Gilbert, 8th edition, figure 6.5(F) + GO:0001759 + We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] + developmentally induced by + + + + + + + + + + + Inverse of developmentally induced by + + developmentally induces + + + + + + + + + + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + false + + In general you should not use this relation to make assertions - use one of the more specific relations below this one + This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from + developmentally preceded by + + + + + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + has chemical role + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + + acts upstream of or within + + + + + + + + + + + x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else + This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage + + replaces + developmentally replaces + + + + + + + + + + Inverse of developmentally preceded by + + developmentally succeeded by + + + + + + + + + + + + + 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue + + + part of developmental precursor of + + + + + + + + + + + x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x + Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. + + ubiquitously expressed in + + + + + + + + + + Inverse of 'expressed in' + + expresses + + + + + + + + + + inverse of ubiquiotously expressed in + + + ubiquitously expresses + + + + + + + + + + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). + This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. + + results in developmental progression of + + + + + + + + + + + every flower development (GO:0009908) results in development of some flower (PO:0009046) + + p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. + + http://www.geneontology.org/GO.doc.development.shtml + + + + results in development of + + + + + + + + + + + an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. + every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) + + + GOC:mtg_berkeley_2013 + + + + results in formation of + + + + + + + + + + an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. + tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) + + The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. + + GOC:mtg_berkeley_2013 + + + + results in morphogenesis of + + + + + + + + + + an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process + bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) + + The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. + + GOC:mtg_berkeley_2013 + + + + results in maturation of + + + + + + + + + foramen ovale closure SubClassOf results in disappearance of foramen ovale + + + May be merged into parent relation + results in disappearance of + + + + + + + + + every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) + + + May be merged into parent relation + results in developmental regression of + + + + + + + + + + Inverse of 'is substance that treats' + + + is treated by substance + + + + + + + + + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' +where +'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview + + x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. + + adapted for living in + + A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. + has habitat + + + + + + + + + + p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. + + + + + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. + + + + + causally upstream of, negative effect + + + + + + + + + A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. + + + + + 2017-06-05T17:35:04Z + has exposure stimulus + + + + + + + + + + evolutionary variant of + + + + + + + + + + Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. + + regulates localization of + + + + transports or maintains localization of + + + + + + + + + + + + + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + characteristic of part of + + + + + + + + + + true + + + + + + + + + + an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. + The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity + + GOC:mtg_berkeley_2013 + + + + results in acquisition of features of + + + + + + + + A relationship that holds via some environmental process + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + evolutionarily related to + + + + + + + + A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) + Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions + + ecologically related to + + + + + + + + + An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. + + adapted for + + confers advantage in + + + + + + + + A mereological relationship or a topological relationship + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to + + + + + + + + A relationship that holds between entities participating in some developmental process (GO:0032502) + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development + developmentally related to + + + + + + + + + Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) + a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. + + In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] + + colocalizes with + + + + + + + + + + ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. + Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. + eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex + We would like to say + +if and only if + exists c', p' + c part_of c' and c' capable_of p + and + c capable_of p' and p' part_of p +then + c contributes_to p + +However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. + + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. + + contributes to + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + c enables p iff c is capable of p and c acts to execute p. + + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + + enables + + + + + + + + A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. + + This is a grouping relation that collects relations used for the purpose of connecting structure and function + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + + false + part of structure that is capable of + + + + + + + + + true + + + + + + + + holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism + genomically related to + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + + actively involved in + enables part of + involved in + + + + + + + + + + every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid + p regulates levels of c if p regulates some amount (PATO:0000070) of c + + + regulates levels of (process to entity) + regulates levels of + + + + + + + + + + inverse of enables + + + enabled by + + + + + + + + + + inverse of regulates + + regulated by (processual) + + regulated by + + + + + + + + + inverse of negatively regulates + + + negatively regulated by + + + + + + + + + inverse of positively regulates + + + positively regulated by + + + + + + + + A relationship that holds via some process of localization + + Do not use this relation directly. It is a grouping relation. + related via localization to + + + + + + + + + + + + + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. + + + + + has target start location + + + + + + + + + + + + + This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. + + + + + has target end location + + + + + + + + + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. + + + imports + + + + + + + + + Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l + + results in transport along + + + + + + + + + + Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. + + + results in transport across + + + + + + + + + + 'pollen tube growth' results_in growth_of some 'pollen tube' + + results in growth of + + + + + + + + + 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) + + results in transport to from or in + + + + + + + + + Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. + + + exports + + + + + + + + + an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. + p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. + + + + + results in commitment to + + + + + + + + + p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. + + + + + results in determination of + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + + + + + + + + + + inverse of has input + + + + input of + + + + + + + + + + inverse of has output + + + + output of + + + + + + + + + + formed as result of + + + + + + + + + + A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. + + results in structural organization of + + + + + + + + + The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. + + + + + results in specification of + + + + + + + + + p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. + + results in developmental induction of + + + + + + + + + + http://neurolex.org/wiki/Property:DendriteLocation + has dendrite location + + + + + + + + + + + a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a + + attached to (anatomical structure to anatomical structure) + + attached to + + + + + + + + + + m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. + + Wikipedia:Insertion_(anatomy) + has muscle origin + + + + + + + + + + + m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. + + Wikipedia:Insertion_(anatomy) + has muscle insertion + + + + + + + + + + false + + x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat + + + has fused element + A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. + derived from ancestral fusion of + + + + + + + + + + A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) + + in branching relationship with + + https://github.com/obophenotype/uberon/issues/170 + + + + + + + + + + Deschutes River tributary_of Columbia River + inferior epigastric vein tributary_of external iliac vein + + x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. + + drains into + drains to + tributary channel of + http://en.wikipedia.org/wiki/Tributary + http://www.medindia.net/glossary/venous_tributary.htm + This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) + + tributary of + + http://en.wikipedia.org/wiki/Tributary + + + + + + + + + + Deschutes River distributary_of Little Lava Lake + + x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x + + branch of + distributary channel of + http://en.wikipedia.org/wiki/Distributary + + This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes + distributary of + + + + + + + + + + + + + + + + + x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. + + anastomoses with + + anabranch of + + + + + + + + + + + + + + + A lump of clay and a statue + x spatially_coextensive_with y if and inly if x and y have the same location + + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios + spatially coextensive with + + + + + + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S + x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y + + + branching part of + + FMA:85994 + + + + + + + + + + In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. + + x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. + + + main stem of + + + + + + + + + + + x proper_distributary_of y iff x distributary_of y and x does not flow back into y + + + proper distributary of + + + + + + + + + + x proper_tributary_of y iff x tributary_of y and x does not originate from y + + + proper tributary of + + + + + + + + + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + + has developmental potential involving + + + + + + + + + + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + + has potential to developmentally contribute to + + + + + + + + + + x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y + + has potential to developmentally induce + + + + + + + + + + x has the potential to develop into y iff x develops into y or if x is capable of developing into y + + has potential to develop into + + + + + + + + + + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + + has potential to directly develop into + + + + + + + + + + + + + 'protein catabolic process' SubClassOf has_direct_input some protein + + p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. + + directly consumes + This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' + has direct input + + + + + + + + + + Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + obsolete has indirect input + true + + + + + + + + translation SubClassOf has_direct_output some protein + + p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. + + directly produces + obsolete has direct output + true + + + + + + + + + + + + + + Likely to be obsoleted. See: +https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit + obsolete has indirect output + true + + + + + + + + + + + + inverse of upstream of + + causally downstream of + + + + + + + + + + + + + immediately causally downstream of + + + + + + + + + This term was obsoleted because it has the same meaning as 'directly positively regulates'. + obsolete directly activates + true + + + + + + + + + + + + + + + + + + + + + + + + + + + p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. + + indirectly activates + + indirectly positively regulates + + + + + + + + + This term was obsoleted because it has the same meaning as 'directly negatively regulates'. + obsolete directly inhibits + true + + + + + + + + + + + + + + + + + + + + + + + p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. + + indirectly inhibits + + indirectly negatively regulates + + + + + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative? + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types. + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causally related to + + + + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + https://en.wikipedia.org/wiki/Causality + + + + + + + + + + + p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. + + + + causally upstream of + + + + + + + + + + p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. + + + immediately causally upstream of + + + + + + + + + + + + + + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. + This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit + + directly provides input for + + directly provides input for (process to process) + provides input for + + + + + + + + + + + transitive form of directly_provides_input_for + + This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. + transitively provides input for (process to process) + transitively provides input for + + + + + + + + + + + p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + + influences (processual) + affects + causally upstream of or within + + + + + + + + false + + This is an exploratory relation + differs in + https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions + + + + + + + + + + differs in attribute of + + + + + + + + + + differs in attribute + + + + + + + + + + inverse of causally upstream of or within + + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + + + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + OWL does not allow defining object properties via a Union + + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + + + + A protein that enables activity in a cytosol. + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + + executes activity in + enables activity in + + is active in + + + + + + + + + true + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + + + + + + + + + p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. + + contributes to morphology of + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Considering relabeling as 'pairwise interacts with' + + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + http://purl.obolibrary.org/obo/MI_0914 + + + + + + + + + + An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) + + genetically interacts with + + http://purl.obolibrary.org/obo/MI_0208 + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + + + An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. + + interacts with on organism level + + biotically interacts with + + http://eol.org/schema/terms/interactsWith + + + + + + + + + An interaction relationship in which the partners are related via a feeding relationship. + + + trophically interacts with + + + + + + + + + + + A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] + Baleen whale preys on krill + An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members + + + + is subject of predation interaction with + preys upon + + preys on + http://eol.org/schema/terms/preysUpon + http://www.inaturalist.org/observations/2942824 + + + + + + + + + + + + + + + + + A biotic interaction in which the two organisms live together in more or less intimate association. + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism + + symbiotically interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + + commensually interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + + mutualistically interacts with + + + + + + + + + + + + + + + + An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). + + http://www.ncbi.nlm.nih.gov/pubmed/19278549 + This relation groups a pair of inverse relations, parasite of and parasitized by + + interacts with via parasite-host interaction + + + + + + + + + + + + + + + + + + Pediculus humanus capitis parasite of human + + parasitizes + direct parasite of + + parasite of + http://eol.org/schema/terms/parasitizes + + + + + + + + + + + has parasite + parasitised by + directly parasitized by + + parasitized by + http://eol.org/schema/terms/hasParasite + + + + + + + + + Porifiera attaches to substrate + A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. + + semibiotically interacts with + + participates in a abiotic-biotic interaction with + + + + + + + + + + + + + + + Axiomatization to GO to be added later + + An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. + phosphorylates + + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + +A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. + + + molecularly controls + directly regulates activity of + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + + + directly inhibits + molecularly decreases activity of + directly negatively regulates activity of + + + + + + + + + + + + + + The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. +For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + + + directly activates + molecularly increases activity of + directly positively regulates activity of + + + + + + + + + all dengue disease transmitted by some mosquito + A relationship that holds between a disease and organism + Add domain and range constraints + + transmitted by + + + + + + + + + A relation that holds between a disease or an organism and a phenotype + + has symptom + + + + + + + + + + The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) + + host of + + + + + + + + + X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y + + + has host + http://eol.org/schema/terms/hasHost + + + + + + + + + + Bees pollinate Flowers + This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. + + is subject of pollination interaction with + + pollinates + http://eol.org/schema/terms/pollinates + + + + + + + + + + has polinator + is target of pollination interaction with + + pollinated by + http://eol.org/schema/terms/hasPollinator + + + + + + + + + + + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. + + acquires nutrients from + + + + + + + + + inverse of preys on + + has predator + is target of predation interaction with + + + preyed upon by + http://eol.org/schema/terms/HasPredator + http://polytraits.lifewatchgreece.eu/terms/PRED + + + + + + + + + + Anopheles is a vector for Plasmodium + + a is a vector for b if a carries and transmits an infectious pathogen b into another living organism + + is vector for + + + + + + + + + + + has vector + + + + + + + + + + Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target + partner in + + + + + + + + + + Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. + subject participant in + + + + + + + + + + Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. + target participant in + + + + + + + + + This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. + helper property (not for use in curation) + + + + + + + + + + is symbiosis + + + + + + + + + + is commensalism + + + + + + + + + + is mutualism + + + + + + + + + + is parasitism + + + + + + + + + + + provides nutrients for + + + + + + + + + + is subject of eating interaction with + + eats + + + + + + + + + + eaten by + is target of eating interaction with + + is eaten by + + + + + + + + + + A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and +the a supports either the existence of b, or the truth value of b. + + + is evidence for + + + + + + + + + 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' + x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. + + + + + composed primarily of + + + + + + + + + ABal nucleus child nucleus of ABa nucleus (in C elegans) + c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d + + This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. + child nucleus of + + + + + + + + + A child nucleus relationship in which the cells are part of a hermaphroditic organism + + child nucleus of in hermaphrodite + + + + + + + + + A child nucleus relationship in which the cells are part of a male organism + + child nucleus of in male + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + + + has part that occurs in + + + + + + + + + true + + + + + + + + + + + + + + An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y + Axiomatization to GO to be added later + + ubiquitinates + + + + + + + + + + is kinase activity + + + + + + + + + + is ubiquitination + + + + + + + + + + See notes for inverse relation + + receives input from + + + + + + + + + This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. + + sends output to + + + + + + + + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. + relation between physical entity and a process or stage + + + + + + + + + + + + + + + + + + x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). + + existence starts during + + + + + + + + + x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). + + existence starts with + + + + + + + + + x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence overlaps + + + + + + + + + + x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) + + exists during + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts and ends during + + + + + + + + + + + + + + + + + + x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during + + + + + + + + + x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends with + + + + + + + + + + x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships + + transformation of + + + + + + + + + + x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t + + + immediate transformation of + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence starts during or after + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. + + The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. + existence ends during or before + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + towards + + + + + + + + + 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate + p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c + + has intermediate product + + has intermediate + + + + + + + + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between entities + + + + + + + + + + + + A coral reef environment is determined by a particular coral reef + s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. + The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future + + + determined by (system to material entity) + + + + determined by + + + + + + + + + inverse of determined by + + determines (material entity to system) + + + determines + + + + + + + + + + + + + + s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. + + + determined by part of + + + + + + + + + true + + + + + + + + + + x is transcribed from y if and only if x is synthesized from template y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + transcribed from + + + + + + + + + inverse of transcribed from + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + transcribed to + + + + + + + + + + x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + ribosomal translation of + + + + + + + + + inverse of ribosomal translation of + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + ribosomally translates to + + + + + + + + A relation that holds between two entities that have the property of being sequences or having sequences. + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. + The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. + + sequentially related to + + + + + + + + + Every UTR is adjacent to a CDS of the same transcript + Two consecutive DNA residues are sequentially adjacent + Two exons on a processed transcript that were previously connected by an intron are adjacent + x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + sequentially adjacent to + + + + + + + + + + + Every CDS has as a start sequence the start codon for that transcript + x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence + + started by + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has start sequence + + + + + + + + + + inverse of has start sequence + + starts + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + + is start sequence of + + + + + + + + + + + Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) + x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence + + ended by + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has end sequence + + + + + + + + + + inverse of has end sequence + + ends + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + + is end sequence of + + + + + + + + + x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. + In the SO paper, this was defined as an instance-type relation + + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + is consecutive sequence of + + + + + + + + + + Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. + x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering + + + is sequentially aligned with + + + + + + + + + + + The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) + x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y + + + bounds sequence of + + + + + + + + + + inverse of bounds sequence of + + + + is bound by sequence of + + + + + + + + + + + + + x has subsequence y iff all of the sequence parts of y are sequence parts of x + + contains + http://www.ncbi.nlm.nih.gov/pubmed/20226267 + + has subsequence + + + + + + + + + + + + inverse of has subsequence + + contained by + + + is subsequence of + + + + + + + + + + + + + + + x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. + + + overlaps sequence of + + + + + + + + + + x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. + + disconnected from + + does not overlap sequence of + + + + + + + + + + inverse of downstream of sequence of + + + is upstream of sequence of + + + + + + + + + + + x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. + + + is downstream of sequence of + + + + + + + + + + A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript + x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y + + + + is immediately downstream of sequence of + + + + + + + + + + A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript + inverse of immediately downstream of + + + is immediately upstream of sequence of + + + + + + + + + + + + Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' + A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. + + has supporting framework + The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). + has skeleton + + + + + + + + + + p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. + + results in ending of + + + + + + + + + + + + + + x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y + Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism + + http://eol.org/schema/terms/hyperparasitoidOf + https://en.wikipedia.org/wiki/Hyperparasite + hyperparasitoid of + epiparasite of + + hyperparasite of + + + + + + + + + + + + + inverse of hyperparasite of + + has epiparasite + has hyperparasite + hyperparasitoidized by + + + hyperparasitized by + + + + + + + + + + http://en.wikipedia.org/wiki/Allelopathy + + allelopath of + http://eol.org/schema/terms/allelopathyYes + x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y + + + + + + + + + + + + pathogen of + + + + + + + + + + + has pathogen + + + + + + + + + inverse of is evidence for + + + + + x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. + has evidence + + + + + + + + + + + + causally influenced by (entity-centric) + causally influenced by + + + + + + + + + + interaction relation helper property + + http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ + + + + + + + + + + molecular interaction relation helper property + + + + + + + + + Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c + + + + + + results in movement of + + + + + + + + + + + + + + + + + + + The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). + + + + causally influences (entity-centric) + causally influences + + + + + + + + + A relation that holds between elements of a musculoskeletal system or its analogs. + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. + biomechanically related to + + + + + + + + + m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. + + Wikipedia:Antagonist_(muscle) + has muscle antagonist + + + + + + + + + + + inverse of branching part of + + + + has branching part + + + + + + + + + x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. + + UBERON:cjm + This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. + + conduit for + + + + + + + + + x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. + + GOC:cjm + + lumen of + + + + + + + + + s is luminal space of x iff s is lumen_of x and s is an immaterial entity + + + luminal space of + + + + + + + + A relation that holds between an attribute or a qualifier and another attribute. + + + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. + + has modifier + + + + + + + + + + + participates in a biotic-biotic interaction with + + + + + + + + + + inverse of has skeleton + + + skeleton of + + + + + + + + + + p directly regulates q iff p is immediately causally upstream of q and p regulates q. + + + directly regulates (processual) + + + + + directly regulates + + + + + + + + + holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y). + existence starts at end of + + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + + has part structure that is capable of + + + + + + + + + + p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. + results in closure of + + + + + + + + + p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p + results in breakdown of + + + + + + + + + results in synthesis of + + + + + + + + + + + + + results in assembly of + + + + + + + + + p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. + results in catabolism of + + + + + + + + + + results in disassembly of + + + + + + + + + + results in remodeling of + + + + + + + + + p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c + results in organization of + + + + + + + + + holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y). + existence ends at start of + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + + pazopanib -> pathological angiogenesis + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. + treats + + The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. + capable of inhibiting or preventing pathological process + + + + + treats + Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship + + + + + + + + + benzene -> cancer [CHEBI] + Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. + causes disease + + capable of upregulating or causing pathological process + + + + + + + + + c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. + treats + + is substance that treats + + + + + + + + + + c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. + May be ceded to OBI + is marker for + + + + + + + + + Inverse of 'causal agent in process' + + process has causal agent + + + + + + + + A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + obsolete related via dependence to + true + + + + + + + + A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Groups both positive and negative correlation + correlated with + + + + + + + + + An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. + A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. + In the Gene Ontology association model, this corresponds to the With/From field + is evidence with support from + + + + + + + + + Inverse of is-model-of + has model + + + + + + + + Do not use this relation directly. It is a grouping relation. + related via evidence or inference to + + + + + + + + + + visits + https://github.com/oborel/obo-relations/issues/74 + + + + + + + + + visited by + + + + + + + + + + visits flowers of + + + + + + + + + has flowers visited by + + + + + + + + + + + lays eggs in + + + + + + + + + + has eggs laid in by + + + + + + + + + + https://github.com/jhpoelen/eol-globi-data/issues/143 + kills + + + + + + + + + is killed by + + + + + + + + + + p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. + + directly positively regulates (process to process) + + + + + directly positively regulates + + + + + + + + + + p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. + + directly negatively regulates (process to process) + + + + + directly negatively regulates + + + + + + + + + + A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host + + ectoparasite of + + + + + + + + + inverse of ectoparasite of + + has ectoparasite + + + + + + + + + + + A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system + lives inside of + endoparasite of + + + + + + + + + has endoparasite + + + + + + + + + + A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite + mesoparasite of + + + + + + + + + inverse of mesoparasite of + + has mesoparasite + + + + + + + + + + A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. + + intercellular endoparasite of + + + + + + + + + inverse of intercellular endoparasite of + + has intercellular endoparasite + + + + + + + + + + A sub-relation of endoparasite-of in which the parasite inhabits host cells. + + intracellular endoparasite of + + + + + + + + + inverse of intracellular endoparasite of + + has intracellular endoparasite + + + + + + + + + + Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. + + co-roosts with + + + + + + + + + + + + + + + + a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. + + + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. + produces + + + + + + + + + a produced_by b iff some process that occurs_in b has_output a. + + + produced by + + + + + + + + + Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. + + represses expression of + + + + + + + + + Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. + + increases expression of + + + + + + + + + + A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. + + is used to study + The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. + has role in modeling + + + + + + + + + The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. + +An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. + Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + causes or contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. + causes condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. + contributes to condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. + contributes to expressivity of condition + contributes to severity of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. + contributes to penetrance of condition + contributes to frequency of condition + + + + + + + + + A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. + is preventative for condition + Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. + +Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. + ameliorates condition + + + + + + + + + A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. + correlated with condition + + + + + + + + + A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. + exacerbates condition + + + + + + + + + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. + condition ameliorated by + + + + + + + + + A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. + condition exacerbated by + + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a more specific relations + + 2017-11-05T02:38:20Z + condition has genetic basis in + + + + + + + + + + + 2017-11-05T02:45:20Z + has material basis in gain of function germline mutation in + + + + + + + + + + + + + 2017-11-05T02:45:37Z + has material basis in loss of function germline mutation in + + + + + + + + + + + 2017-11-05T02:45:54Z + has material basis in germline mutation in + + + + + + + + + + + + 2017-11-05T02:46:07Z + has material basis in somatic mutation in + + + + + + + + + + + + 2017-11-05T02:46:26Z + has major susceptibility factor + + + + + + + + + + + 2017-11-05T02:46:57Z + has partial material basis in germline mutation in + + + + + + + + + p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. + + 2018-12-13T11:26:17Z + + has primary input or output + + + + + + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + + 2018-12-13T11:26:32Z + + has primary output + + + + + p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + + 2018-12-13T11:26:56Z + + has primary input + + + + + p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. + GOC:cjm + GOC:dph + GOC:kva + GOC:pt + PMID:27812932 + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a more specific relations + + 2017-11-05T02:53:08Z + is genetic basis for condition + + + + + + + + + Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:55:51Z + is causal gain of function germline mutation of in + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:56:06Z + is causal loss of function germline mutation of in + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:56:40Z + is causal germline mutation in + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. + + 2017-11-05T02:57:07Z + is causal somatic mutation in + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. + + 2017-11-05T02:57:43Z + is causal susceptibility factor for + + + + + + + + + + + Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. + + 2017-11-05T02:58:43Z + is causal germline mutation partially giving rise to + + + + + + + + + + + + 2017-11-05T03:20:01Z + realizable has basis in + + + + + + + + + + 2017-11-05T03:20:29Z + is basis for realizable + + + + + + + + + + + 2017-11-05T03:26:47Z + disease has basis in + + + + + + + + + A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. + disease has basis in dysfunction of (disease to anatomical structure) + + 2017-11-05T03:29:32Z + disease has basis in dysfunction of + + + + + + + + + A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. + disease has basis in disruption of (disease to process) + + 2017-11-05T03:37:52Z + disease has basis in disruption of + + + + + + + + + + A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. + + 2017-11-05T03:46:07Z + disease has basis in feature + + + + + + + + + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. + + 2017-11-05T03:50:54Z + causal relationship with disease as subject + + + + + + + + + + + + + + + + + A relationship between a disease and a process where the disease process disrupts the execution of the process. + disease causes disruption of (disease to process) + + 2017-11-05T03:51:09Z + disease causes disruption of + + + + + + + + + + + + + disease causes dysfunction of (disease to anatomical entity) + + 2017-11-05T03:58:20Z + disease causes dysfunction of + + + + + + + + + A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. + TODO: complete range axiom once more of CARO has been mireoted in to this ontology + This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. + + 2017-11-05T04:06:02Z + disease has location + + + + + + + + + A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity + + 2017-12-26T19:37:31Z + disease has inflammation site + + + + + + + + + + + + + A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. + + 2017-12-26T19:45:49Z + realized in response to stimulus + + + + + + + + + A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. + + 2017-12-26T19:50:53Z + disease has feature + + + + + + + + + A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. + + 2017-12-26T19:58:44Z + disease arises from alteration in structure + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + + 2018-01-25T23:20:13Z + enables subfunction + + + + + + + + + + + + + + + 2018-01-26T23:49:30Z + + acts upstream of or within, positive effect + + + + + + + + + + + + + + + + 2018-01-26T23:49:51Z + + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + + 2018-01-26T23:53:14Z + + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + + 2018-01-26T23:53:22Z + + acts upstream of, negative effect + + + + + + + + + + + + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. + DEPRECATED inheres in + true + + + + + + + + DEPRECATED bearer of + true + + + + + + + + A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity. + + has driver + + + + + + + + + + A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes. + + has disease driver + + + + + + + + + + + An interaction relationship wherein a plant or algae is living on the outside surface of another plant. + https://en.wikipedia.org/wiki/Epiphyte + epiphyte of + + + + + + + + + inverse of epiphyte of + + has epiphyte + + + + + + + + + + A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material + https://en.wikipedia.org/wiki/Kleptoparasitism + kleptoparasite of + + + + + + + + + inverse of kleptoparasite of + + kleptoparasitized by + + + + + + + + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. + creates habitat for + + + + + + + + + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. + ecologically co-occurs with + + + + + + + + + + An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. + lays eggs on + + + + + + + + + inverse of lays eggs on + has eggs laid on by + + + + + + + + + muffin 'has substance added' some 'baking soda' + + "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. + The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. + + has substance added + + + + + + + + + 'egg white' 'has substance removed' some 'egg yolk' + + "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. + + has substance removed + + + + + + + + + sardines 'immersed in' some 'oil and mustard' + + "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. + + immersed in + + + + + + + + sardine has consumer some homo sapiens + + 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. + + has consumer + + + + + + + + + + bread 'has primary substance added' some 'flour' + + 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. + + has primary substance added + + + + + + + + + + + + + A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. + An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) + Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. + r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. + + + + + triggered by process + realized in response to + https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit + + + + + triggered by process + RO:cjm + + + + + + + + + + + + + Genetic information generically depend on molecules of DNA. + The novel *War and Peace* generically depends on this copy of the novel. + The pattern shared by chess boards generically depends on any chess board. + The score of a symphony g-depends on a copy of the score. + This pdf file generically depends on this server. + A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. + [072-ISO] + g-depends on + generically depends on + + + + + + + + + + + + Molecules of DNA are carriers of genetic information. + This copy of *War and Peace* is carrier of the novel written by Tolstoy. + This hard drive is carrier of these data items. + *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* + [072-ISO] + is carrier of + + + + + + + + + The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. + + regulates activity of + + + + + + + + + The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. + + regulates quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. + + indirectly regulates activity of + + + + + + + + + The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. + +For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. + + decreases by repression quantity of + + + + + + + + + The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. + +For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. + + increases by expression quantity of + + + + + + + + + The entity A has an activity that directly positively regulates the quantity of B. + + directly positively regulates quantity of + + + + + + + + + The entity A has an activity that directly negatively regulates the quantity of B. + + directly negatively regulates quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. + + indirectly activates + indirectly positively regulates activity of + + + + + + + + + AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) + An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. + + destabilizes quantity of + + + + + + + + + AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) + An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. + + stabilizes quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. + + indirectly inhibits + indirectly negatively regulates activity of + + + + + + + + + The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. + + directly regulates quantity of + + + + + + + + + The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. + + indirectly regulates quantity of + + + + + + + + + The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. + + indirectly negatively regulates quantity of + + + + + + + + + The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. + + indirectly positively regulates quantity of + + + + + + + + + + a relation between a process and a continuant, in which the process is regulated by the small molecule continuant + pg + 2020-04-22T20:27:26Z + has small molecule regulator + + + + + + + + + + a relation between a process and a continuant, in which the process is activated by the small molecule continuant + pg + 2020-04-22T20:28:37Z + has small molecule activator + + + + + + + + + + a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant + pg + 2020-04-22T20:28:54Z + has small molecule inhibitor + + + + + + + + + p acts on population of c iff c' is a collection, has members of type c, and p has participant c + pg + 2020-06-08T17:21:33Z + + + + acts on population of + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process + pg + 2020-06-24T13:15:17Z + is small molecule regulator of + + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that activates the process + pg + 2020-06-24T13:15:26Z + is small molecule activator of + + + + + + + + + + a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process + pg + 2020-06-24T13:15:35Z + is small molecule inhibitor of + + + + + + + + + The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. + pg + 2020-08-27T08:13:59Z + results in adhesion of + + + + + + + + + pg + 2021-02-26T07:28:29Z + + + + results in fusion of + + + + + + + + + p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. + pg + 2022-09-26T06:01:01Z + + + constitutively upstream of + + + + + + + + + p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. + pg + 2022-09-26T06:06:20Z + + + removes input for + + + + + + + + + p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. + pg + 2022-09-26T06:07:17Z + indirectly causally upstream of + + + + + + + + + + p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. + pg + 2022-09-26T06:08:01Z + indirectly regulates + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. + + 2020-07-17T09:26:52Z + has synaptic input or output in + has synaptic IO in region + + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. + + 2020-07-17T09:42:23Z + receives synaptic input in region + + + + + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. + + 2020-07-17T09:45:06Z + sends synaptic output to region + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:52:19Z + has synaptic IO throughout + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:55:36Z + receives synaptic input throughout + + + + + + + + + + A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). + + 2020-07-17T09:57:27Z + sends synaptic output throughout + + + + + + + + + + + + + Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. + + 2020-07-20T12:10:09Z + has sensory dendrite location + has sensory terminal in + has sensory terminal location + has sensory dendrite in + + + + + + + + + + A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. + + 2021-05-26T08:40:18Z + receives synaptic input from neuron + + + + + + + + + A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. + + 2021-05-26T08:41:07Z + Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. + sends synaptic output to cell + + + + + + + + + A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. + + disease has infectious agent + + + + + + + + + + + + + transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) + A relation between a material entity and some data in which the data is taken as exemplifying the material entity. + C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. + + This relation is not meant to capture the relation between occurrents and data. + has exemplar data + + + + + + + + + exemplar data of + + + + + + + + + + A relation between a group and another group it is part of but does not fully constitute. + X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. + + This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. + subcluster of + + + + + + + + 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1'). + transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3. + A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. + C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. + This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. + + has marker gene combination + has marker signature set + has characterizing marker set + + + + + + + + q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + different in magnitude relative to + + + + + q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. + increased in magnitude relative to + + + + + q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. + decreased in magnitude relative to + + + + + q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + similar in magnitude relative to + + + + + q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + has relative magnitude + + + + + + + + s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. + Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. + has cross section + + + + + s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. + There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. + reciprocal of + + + + + q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. + https://orcid.org/0000-0002-6601-2165 + + + + + + + + + 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') + A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. + + + has high plasma membrane amount + + + + + A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. + PMID:19243617 + + + + + + + + + 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') + A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. + + + has low plasma membrane amount + + + + + A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. + PMID:19243617 + + + + + + + + Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. + + 2021-11-05T17:30:14Z + has phenotype or disease + https://github.com/oborel/obo-relations/issues/478 + + + + + + + + + A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. + + 2021-11-05T17:30:44Z + has disease + https://github.com/oborel/obo-relations/issues/478 + + + + + + + + + X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. + ExO:0000083 + 2021-12-14T20:41:45Z + + has exposure medium + + + + + + + + + + + + A diagnostic testing device utilizes a specimen. + X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. + + + A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. + See github ticket https://github.com/oborel/obo-relations/issues/497 + 2021-11-08T12:00:00Z + utilizes + device utilizes material + + + + + + + + + Helper relation for OWL definition of RO:0018002 myristoylates + + is myristoyltransferase activity + + + + + + + + + + + + + + + A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input + + + myristoylates + + + + + + + + inverse of myristoylates + + myristoylated by + + + + + + + + + mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor + + is agonist of + + + + + + + + + + pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level + + is inverse agonist of + + + + + + + + + + tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) + a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level + + is antagonist of + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. + + regulates characteristic + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. + + positively regulates characteristic + + + + + + + + + + + + + + + + + A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. + + negatively regulates characteristic + + + + + + + + + Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. + + confers susceptibility to condition + + + + + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + + 2018-09-26T00:00:32Z + disease relationship + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + + 2018-09-26T01:08:58Z + results in changes to anatomical or cellular structure + + + + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + TODO: Add homeomorphy axiom + + + + + ECO:0000041 + SO:similar_to + sameness + similar to + correspondence + resemblance + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + + + + + + + + + + + + Similarity that results from common evolutionary origin. + + + homologous to + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + + + + + + + + + + + + + Similarity that results from independent evolution. + + + homoplasous to + analogy + in homoplasy relationship with + + + + + + Similarity that results from independent evolution. + + + + + + + + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + ECO:0000075 + homocracous to + Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + in homocracy relationship with + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + + + + + + + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + analogy + Convergence usually implies a notion of adaptation. + in convergence relationship with + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + + + + + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + parallel evolution + Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + in parallelism relationship with + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + + + + + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + ECO:0000071 + MI:2163 + structural homologous to + idealistic homology + in structural homology relationship with + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by common descent. + + + homology + ECO:0000080 + RO_proposed_relation:homologous_to + SO:0000330 + SO:0000853 + SO:0000857 + SO:homologous_to + TAO:homologous_to + cladistic homology + historical homologous to + phylogenetic homology + taxic homology + true homology + in historical homology relationship with + + + + + + Homology that is defined by common descent. + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + ECO:0000067 + biological homologous to + transformational homology + Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + in biological homology relationship with + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + + + + + + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + atavism + rudiment + reversion + in reversal relationship with + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + + + + + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + + MeSH:Synteny + SO:0000860 + SO:0005858 + syntenic homologous to + synteny + in syntenic homology relationship with + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + MeSH:Synteny + + + + + + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + SO:0000854 + SO:0000859 + SO:paralogous_to + paralogous to + in paralogy relationship with + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + + + + + + + + + + + + + Paralogy that involves sets of syntenic blocks. + + + syntenic paralogous to + duplicon + paralogon + in syntenic paralogy relationship with + + + + + + Paralogy that involves sets of syntenic blocks. + + + DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y + + + + + + + + + + Syntenic homology that involves chromosomes of different species. + + + syntenic orthologous to + in syntenic orthology relationship with + + + + + + Syntenic homology that involves chromosomes of different species. + + + + + + + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + + fractional homology + partial homologous to + segmental homology + mixed homology + modular homology + partial correspondence + percent homology + in partial homology relationship with + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + ISBN:0123195837 + ISBN:978-0471984931 + + + + + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + MeSH:Structural_Homology,_Protein + protein structural homologous to + in protein structural homology relationship with + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + + + + + + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + + pseudogene + SO:non_functional_homolog_of + non functional homologous to + in non functional homology relationship with + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + SO:non_functional_homolog_of + + + + + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + ECO:00000060 + SO:0000855 + SO:0000858 + SO:orthologous_to + orthologous to + The term is sometimes also used for anatomical structures. + in orthology relationship with + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + + + + + + + + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + xenologous to + The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + in xenology relationship with + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + + + + + + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + + 1 to 1 homologous to + 1:1 homology + one-to-one homology + in 1 to 1 homology relationship with + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + BGEE:curator + + + + + + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + 1 to 1 orthologous to + 1:1 orthology + one-to-one orthology + in 1 to 1 orthology relationship with + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + + + + + + + + + + + Paralogy that results from a whole genome duplication event. + + + ohnologous to + homoeology + in ohnology relationship with + + + + + + Paralogy that results from a whole genome duplication event. + + + + + + + + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + in-paralogous to + inparalogy + symparalogy + in in-paralogy relationship with + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + + + + + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + alloparalogy + out-paralogous to + outparalogy + in out-paralogy relationship with + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + + + + + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + pro-orthologous to + in pro-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + + + + + + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + semi-orthologous to + The converse of pro-orthologous. + in semi-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + + + + + + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + serial homologous to + homonomy + in serial homology relationship with + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + + + + + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + + heterochronous homologous to + heterochrony + in heterochronous homology relationship with + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + ISBN:978-0674639416 + + + + + + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + juvenification + pedomorphosis + in paedomorphorsis relationship with + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + ISBN:978-0674639416 + + + + + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + in peramorphosis relationship with + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + + + + + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + in progenesis relationship with + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + ISBN:978-0674639416 + + + + + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + juvenilization + neotenous to + in neoteny relationship with + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + ISBN:978-0674639416 + + + + + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + mimicrous to + in mimicry relationship with + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + + + + + + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + 1 to many orthologous to + 1:many orthology + one-to-many orthology + co-orthology + many to 1 orthology + in 1 to many orthology relationship with + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + + + + + + + + + + + Historical homology that involves two members of a larger set of homologs. + + + many to many homologous to + many-to-many homology + many:many homology + in many to many homology relationship with + + + + + + Historical homology that involves two members of a larger set of homologs. + + + + + + + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + + 1 to many homologous to + one-to-many homology + 1:many homology + in 1 to many homology relationship with + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + BGEE:curator + + + + + + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + + apomorphous to + synapomorphy + in apomorphy relationship with + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + ISBN:978-0252068140 + + + + + + + + + + Historical homology that is based on distant shared ancestry. + + + plesiomorphous to + symplesiomorphy + This term is usually contrasted to apomorphy. + in plesiomorphy relationship with + + + + + + Historical homology that is based on distant shared ancestry. + + ISBN:978-0252068140 + + + + + + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + deep genetic homology + deep homologous to + generative homology + homoiology + Used for structures in distantly related taxa. + in deep homology relationship with + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + + + + + + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + hemiplasous to + in hemiplasy relationship with + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + + + + + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + gametologous to + in gametology relationship with + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + + + + + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + + MeSH:Chromosome_Pairing + chromosomal homologous to + in chromosomal homology relationship with + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + ISBN:0195307615 + + + + + + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + many to many orthologous to + many-to-many orthology + many:many orthology + trans-orthology + co-orthology + trans-homology + in many to many orthology relationship with + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + + + + + + + + + + + + Paralogy that involves genes from the same species. + + + within-species paralogous to + in within-species paralogy relationship with + + + + + + Paralogy that involves genes from the same species. + + + + + + + + + + + + Paralogy that involves genes from different species. + + + between-species paralogous to + The genes have diverged before a speciation event. + in between-species paralogy relationship with + + + + + + Paralogy that involves genes from different species. + + + + + + + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + post-displacement + in postdisplacement relationship with + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + + + + + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + in hypermorphosis relationship with + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + ISBN:978-0674639416 + + + + + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + synologous to + in synology relationship with + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + + + + + + + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + ECO:0000080 + isoorthologous to + in isoorthology relationship with + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + tandem paralogous to + iterative paralogy + serial paralogy + in tandem paralogy relationship with + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + ISBN:978-0878932665 + + + + + + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + apomorphic tendency + cryptic homology + latent homologous to + underlying synapomorphy + homoiology + homoplastic tendency + re-awakening + Used for structures in closely related taxa. + in latent homology relationship with + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + + + ISBN:0199141118 + + + + + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + generative homology + syngenous to + Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + in syngeny relationship with + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R + + + + + + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + 1:1 paralogy + apparent 1:1 orthology + apparent orthologous to + pseudoorthology + The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + in apparent orthology relationship with + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + + + + + + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + pseudoparalogous to + These genes may come out as paralogs in a single-genome analysis. + in pseudoparalogy relationship with + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + + + + + + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + equivalogous to + This may include examples of orthology, paralogy and xenology. + in equivalogy relationship with + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + interologous to + in interology relationship with + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + + + + + + + + + + + Similarity that is characterized by interchangeability in function. + + + functional similarity + in functional equivalence relationship with + + + + + + Similarity that is characterized by interchangeability in function. + + + + + + + + + + + + + Biological homology that involves parts of the same organism. + + + iterative homologous to + in iterative homology relationship with + + + + + + Biological homology that involves parts of the same organism. + + + + + + + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + duplicate xenology + multiple xenology + paraxenologous to + in paraxenology relationship with + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + + + + + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + plerologous to + This phenomenon is usually due to gene conversion process. + in plerology relationship with + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + + + + + + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + homotopous to + Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + in homotopy relationship with + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + + ISBN:0123195837 + + + + + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + heterotopy + in homeosis relationship with + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + + + + + + + + + + + + Synology that results from allopolyploidy. + + + homoeologous to + On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + in homoeology relationship with + + + + + + Synology that results from allopolyploidy. + + + + + + + + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + axis paramorphism + in paramorphism relationship with + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + + + + + + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + regulogous to + in regulogy relationship with + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + + + + + + + + + + + + + + + + + + 0 + + + 100 + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + dos + 2018-05-22T16:43:28Z + This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. + has increased age-specific mortality rate + + + + + Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. + PMID:24138933 + Wikipedia:Infant_mortality + + + + + + + + + + + + + ## Elucidation + +This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; + +## How to interpret (informal) + +First the &quot;atemporal&quot; FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + axiom holds for all times + + + + + + + + ## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y) + relation has no temporal argument + + + + + + + + + curation status specification + + + + ready for release + + + + pending final vetting + + + + obsolescence reason specification + + + + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-chado.tsv b/subsets/ro-chado.tsv new file mode 100644 index 00000000..e69de29b diff --git a/subsets/ro-developmental.json b/subsets/ro-developmental.json new file mode 100644 index 00000000..4c466e7e --- /dev/null +++ b/subsets/ro-developmental.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-developmental.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_2D_boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_2D_boundary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "lbl" : "electrically_synapsed_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions." + }, + "xrefs" : [ { + "val" : "RO:0002003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "electrically_synapsed_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002007" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "lbl" : "coincident with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." + }, + "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002008" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note from NCEAS meeting: consider changing primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "coincident_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "lbl" : "regulates in other organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "xrefs" : [ { + "val" : "RO:0002010" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_in_other_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "lbl" : "occurrent part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A part of relation that applies only between occurrents." + }, + "xrefs" : [ { + "val" : "RO:0002012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurrent_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." + }, + "xrefs" : [ { + "val" : "RO:0002013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "xrefs" : [ { + "val" : "RO:0002014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_negative_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], + "xrefs" : [ { + "val" : "RO:0002015" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_positive_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "lbl" : "has necessary component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], + "xrefs" : [ { + "val" : "RO:0002016" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_necessary_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], + "xrefs" : [ { + "val" : "RO:0002017" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:44:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "xrefs" : [ { + "val" : "RO:0002018" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "lbl" : "has ligand", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." + }, + "xrefs" : [ { + "val" : "RO:0002019" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-19T17:30:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ligand" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "lbl" : "transports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." + }, + "xrefs" : [ { + "val" : "RO:0002020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:11:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." + }, + "xrefs" : [ { + "val" : "RO:0002021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "xrefs" : [ { + "val" : "RO:0002022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:38Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "xrefs" : [ { + "val" : "RO:0002085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "di" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "encompasses" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_after" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "xrefs" : [ { + "val" : "RO:0002087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "lbl" : "during which starts", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." + }, + "xrefs" : [ { + "val" : "RO:0002104" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : 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"synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002106" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that 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I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 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}, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002297" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002298" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_morphogenesis_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_maturation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002300" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_disappearance_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002301" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_regression_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002302" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_treated_by_substance" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002303" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_habitat" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002304" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002305" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002309" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stimulus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002313" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports_or_maintains_localization_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "xrefs" : [ { + "val" : "RO:0002314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : 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"http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_acquisition_of_features_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002321" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "colocalizes_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002326" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002327" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enables" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "xrefs" : [ { + "val" : "RO:0002328" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "functionally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "xrefs" : [ { + "val" : "RO:0002329" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_structure_that_is_capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "xrefs" : [ { + "val" : "RO:0002331" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "xrefs" : [ { + "val" : "RO:0002332" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_levels_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002333" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enabled_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002334" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002335" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002336" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "xrefs" : [ { + "val" : "RO:0002337" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_localization_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002338" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002339" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002340" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "imports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "xrefs" : [ { + "val" : "RO:0002341" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_along" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002342" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002343" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_growth_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002344" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' 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"http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "exports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002348", + "lbl" : "results in commitment to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002348" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. 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It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. 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"RO:0002445" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitized_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. 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We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "subject_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002463" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "target_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002469" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_nutrients_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002470" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "eats" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002471" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_eaten_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002473" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "composed_primarily_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "xrefs" : [ { + "val" : "RO:0002476" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/subsets/ro-developmental.obo b/subsets/ro-developmental.obo index 0d29373a..f8e39bda 100644 --- a/subsets/ro-developmental.obo +++ b/subsets/ro-developmental.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-developmental -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/subsets/ro-developmental.owl b/subsets/ro-developmental.owl index 27c2e134..a7ea63b4 100644 --- a/subsets/ro-developmental.owl +++ b/subsets/ro-developmental.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-developmental.tsv b/subsets/ro-developmental.tsv new file mode 100644 index 00000000..42281381 --- /dev/null +++ b/subsets/ro-developmental.tsv @@ -0,0 +1,51 @@ +?x ?label +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid1 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid18 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid22 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid26 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid33 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid37 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid40 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid5 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid52 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid58 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid61 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid64 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid67 +_:B62f211d8X2D868aX2D4b4aX2D9f95X2D732551044d53genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-eco.json b/subsets/ro-eco.json new file mode 100644 index 00000000..ad70b049 --- /dev/null +++ b/subsets/ro-eco.json @@ -0,0 +1,13048 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-eco.owl", + "meta" : { + "version" : "http://purl.obolibrary.org/obo/ro/http://purl.obolibrary.org/obo/ro-edit.owl/subsets/ro-eco.owl" + }, + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", 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via a series of synaptically connected neurons." + }, + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000301", + "lbl" : "obsolete upstream in neural circuit with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first." + }, + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000302", + "lbl" : "obsolete downstream in neural circuit with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first." + }, + "comments" : [ "Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other)." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001018", + "lbl" : "contained in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "contained in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001019", + "lbl" : "contains", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "contains" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", 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response against the material entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001900", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002001", + "lbl" : "aligned with", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be obsoleted, see https://github.com/oborel/obo-relations/issues/260" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "lbl" : "electrically_synapsed_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002004", + "lbl" : "tracheates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002005", + "lbl" : "innervated_by", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "lbl" : "coincident with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." + }, + "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note from NCEAS meeting: consider changing primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002009", + "lbl" : "cell expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "x 'cell expresses' y iff:\ncell(x)\nAND gene(y)\nAND exists some 'transcription, DNA templated (GO_0006351)'(t)\nAND t occurs_in x\nAND t has_input y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "lbl" : "regulates in other organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002011", + "lbl" : "regulates transport of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a process that regulates a transport process and the entity transported by that process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "lbl" : "occurrent part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A part of relation that applies only between occurrents." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "lbl" : "has necessary component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:44:33Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "lbl" : "has ligand", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-19T17:30:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "lbl" : "transports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:11:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:38Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002029", + "lbl" : "has increased age-specific mortality rate", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population.", + "xrefs" : [ "PMID:24138933", "Wikipedia:Infant_mortality" ] + }, + "comments" : [ "This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-05-22T16:43:28Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "di" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002105", + "lbl" : "synapsed_via_type_Ib_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton." + }, + "comments" : [ "Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002106", + "lbl" : "synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002107", + "lbl" : "synapsed_via_type_II_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type II bouton." + }, + "comments" : [ "Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002108", + "lbl" : "synapsed_by_via_type_II_bouton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type II bouton." + }, + "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002109", + "lbl" : "synapsed_by_via_type_Ib_bouton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton." + }, + "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002110", + "lbl" : "has postsynaptic terminal in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "synapsed in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002111", + "lbl" : "releases neurotransmitter", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has neurotransmitter" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002112", + "lbl" : "synapsed_by_via_type_Is_bouton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], + "basicPropertyValues" : [ { + "pred" : 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neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "synapses in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002114", + "lbl" : "synapsed_via_type_III_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." + }, + "comments" : [ "Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002115", + "lbl" : "synapsed_by_via_type_III_bouton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a muscle and a motor neuron that synapses to it via a type III bouton.\n" + }, + "comments" : [ "Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y)))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002120", + "lbl" : "synapsed to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " + }, + "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002121", + "lbl" : "dendrite synapsed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.\n\n\t" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n\t and some (\n\t http://purl.obolibrary.org/obo/GO_0042734 and some (\n\t and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002130", + "lbl" : "has synaptic terminal in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : 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"id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" 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some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that ( some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "lbl" : "derived by descent from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral_stucture_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "evolutionarily_descended_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "lbl" : "has derived by descendant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of derived by descent from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "lbl" : "serially homologous to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + }, + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9227-417X" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002171", + "lbl" : "mutually spatially disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "non-overlapping with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no parts with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX owl: \nPREFIX part_of: \nPREFIX mutually_spatially_disjoint_with: \nCONSTRUCT {\n part_of: a owl:ObjectProperty .\n [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?x ;\n owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty part_of: ;\n owl:someValuesFrom ?y\n ]\n ]\n}\nWHERE {\n ?x mutually_spatially_disjoint_with: ?y .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/RO_0002163" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002172", + "lbl" : "taxonomic class assertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002173", + "lbl" : "ambiguous for taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg]" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002174", + "lbl" : "dubious for taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T." + }, + "comments" : [ "This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" + }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002204", + "lbl" : "gene product of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002205", + "lbl" : "has gene product", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every HOTAIR lncRNA is the gene product of some HOXC gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002214", + "lbl" : "has prototype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a \"canonical\" heart, which participates in blood circulation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002217", + "lbl" : "obsolete actively participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" + }, + "comments" : [ "Obsoleted as the inverse property was obsoleted." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "agent in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002608" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002218", + "lbl" : "obsolete has active participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has agent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002500" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002245", + "lbl" : "over-expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002246", + "lbl" : "under-expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "lbl" : "defined by inverse", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002291", + "lbl" : "ubiquitously expressed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'expressed in'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002293", + "lbl" : "ubiquitously expresses", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ubiquiotously expressed in" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002312", + "lbl" : "evolutionary variant of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" + }, { + "pred" : 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changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002349", + "lbl" : "results in determination of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "lbl" : "input of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has input" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "lbl" : "output of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has output" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "lbl" : "formed as result of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002355", + "lbl" : "results in structural organization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002356", + "lbl" : "results in specification of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002374", + "lbl" : "derived from ancestral fusion of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" + }, + "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "has fused element" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002401", + "lbl" : "obsolete has indirect input", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002402", + "lbl" : "obsolete has direct output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "translation SubClassOf has_direct_output some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly produces" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002403", + "lbl" : "obsolete has indirect output", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002406", + "lbl" : "obsolete directly activates", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly positively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002629" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002408", + "lbl" : "obsolete directly inhibits", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This term was obsoleted because it has the same meaning as 'directly negatively regulates'." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0002630" + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002416", + "lbl" : "logical macro assertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002419", + "lbl" : "annotation property cardinality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002420", + "lbl" : "logical macro assertion on a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a class" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002421", + "lbl" : "logical macro assertion on a property", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A logical macro assertion whose domain is an IRI for a property" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002422", + "lbl" : "logical macro assertion on an object property", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Used to annotate object properties to describe a logical meta-property or characteristic of the object property." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002423", + "lbl" : "logical macro assertion on an annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002424", + "lbl" : "differs in", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "This is an exploratory relation" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002425", + "lbl" : "differs in attribute of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002426", + "lbl" : "differs in attribute", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000316" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0208" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002436", + "lbl" : "molecularly interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "binds" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "molecularly binds with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ECO_0000353" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0915" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002437", + "lbl" : "biotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "interacts with on organism level" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/interactsWith" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002438", + "lbl" : "trophically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which the partners are related via a feeding relationship." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002439", + "lbl" : "preys on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Baleen whale preys on krill" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7134-3324" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-3138-4118" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of predation interaction with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preys upon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/preysUpon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.inaturalist.org/observations/2942824" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002440", + "lbl" : "symbiotically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction in which the two organisms live together in more or less intimate association." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002441", + "lbl" : "commensually interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002442", + "lbl" : "mutualistically interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002443", + "lbl" : "interacts with via parasite-host interaction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19278549" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation groups a pair of inverse relations, parasite of and parasitized by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002444", + "lbl" : "parasite of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "direct parasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Pediculus humanus capitis parasite of human" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitizes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/parasitizes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002445", + "lbl" : "parasitized by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "directly parasitized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "semibiotically interacts with" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Porifiera attaches to substrate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002447", + "lbl" : "phosphorylates", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002448", + "lbl" : "directly regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly decreases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly inhibits" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002450", + "lbl" : "directly positively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly increases activity of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly activates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002451", + "lbl" : "transmitted by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a disease and organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "all dengue disease transmitted by some mosquito" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Add domain and range constraints" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002452", + "lbl" : "has symptom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between a disease or an organism and a phenotype" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002453", + "lbl" : "host of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002454", + "lbl" : "has host", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasHost" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002455", + "lbl" : "pollinates", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Bees pollinate Flowers" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/pollinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002456", + "lbl" : "pollinated by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has polinator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of pollination interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasPollinator" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002457", + "lbl" : "acquires nutrients from", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002458", + "lbl" : "preyed upon by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of preys on" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has predator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of predation interaction with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/HasPredator" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://polytraits.lifewatchgreece.eu/terms/PRED" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002459", + "lbl" : "is vector for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Anopheles is a vector for Plasmodium" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "a is a vector for b if a carries and transmits an infectious pathogen b into another living organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002460", + "lbl" : "has vector", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002461", + "lbl" : "partner in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002462", + "lbl" : "subject participant in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002464", + "lbl" : "helper property (not for use in curation)", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002465", + "lbl" : "is symbiosis", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002466", + "lbl" : "is commensalism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002467", + "lbl" : "is mutualism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002468", + "lbl" : "is parasitism", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002472", + "lbl" : "is evidence for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and \nthe a supports either the existence of b, or the truth value of b." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002474", + "lbl" : "dispositional interpretation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002475", + "lbl" : "has no connections with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is has_no_connections_with B if there are no parts of A or B that have a connection with the other." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "shares no connection with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", + "val" : "Class: EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002481", + "lbl" : "is kinase activity", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002482", + "lbl" : "is ubiquitination", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002483", + "lbl" : "inherited annotation property", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002484", + "lbl" : "curator guidance link", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "exists during" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/BFO_0000169" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002503", + "lbl" : "towards", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002504", + "lbl" : "always present in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "brain always_present_in_taxon 'Vertebrata'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "forelimb always_present_in_taxon Euarchontoglires" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "never lost in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002505", + "lbl" : "has intermediate", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has intermediate product" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002506", + "lbl" : "causal relation between entities", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002507", + "lbl" : "determined by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A coral reef environment is determined by a particular coral reef" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/24330602" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determined by (system to material entity)" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002508", + "lbl" : "determines", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of determined by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "determines (material entity to system)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002509", + "lbl" : "determined by part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002510", + "lbl" : "transcribed from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is transcribed from y if and only if x is synthesized from template y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002511", + "lbl" : "transcribed to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of transcribed from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002512", + "lbl" : "ribosomal translation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002513", + "lbl" : "ribosomally translates to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ribosomal translation of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002514", + "lbl" : "sequentially related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two entities that have the property of being sequences or having sequences. " + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are sequentially adjacent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two exons on a processed transcript that were previously connected by an intron are adjacent" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002516", + "lbl" : "has start sequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002518", + "lbl" : "has end sequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ended by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002519", + "lbl" : "is end sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has end sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002520", + "lbl" : "is consecutive sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "In the SO paper, this was defined as an instance-type relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002521", + "lbl" : "is sequentially aligned with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002522", + "lbl" : "bounds sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002523", + "lbl" : "is bound by sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of bounds sequence of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002524", + "lbl" : "has subsequence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has subsequence y iff all of the sequence parts of y are sequence parts of x" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contains" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002525", + "lbl" : "is subsequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has subsequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contained by" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002526", + "lbl" : "overlaps sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002527", + "lbl" : "does not overlap sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "disconnected from" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002528", + "lbl" : "is upstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of downstream of sequence of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002529", + "lbl" : "is downstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002530", + "lbl" : "is immediately downstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002529" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002531", + "lbl" : "is immediately upstream of sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of immediately downstream of" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002535", + "lbl" : "temporal logical macro assertion on a class", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This properties were created originally for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. " + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002536", + "lbl" : "measurement property has unit", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002537", + "lbl" : "has start time value", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002538", + "lbl" : "has end time value", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002539", + "lbl" : "start, days post fertilization", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002540", + "lbl" : "end, days post fertilization", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002541", + "lbl" : "start, years post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002542", + "lbl" : "end, years post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002543", + "lbl" : "start, months post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002544", + "lbl" : "end, months post birth", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002545", + "lbl" : "month of gestation", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002546", + "lbl" : "has developmental stage marker", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002547", + "lbl" : "start, days post coitum", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the start of the stage and the time of coitum." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum)" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002548", + "lbl" : "end, days post coitum", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Count of number of days intervening between the end of the stage and the time of coitum." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002549", + "lbl" : "start, weeks post birth", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002550", + "lbl" : "end, weeks post birth", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/temporal-durations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002551", + "lbl" : "has skeleton", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has supporting framework" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002552", + "lbl" : "results in ending of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002553", + "lbl" : "hyperparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "hyperparasitoid of" + }, { + "pred" : "hasRelatedSynonym", + "val" : "epiparasite of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://eol.org/schema/terms/hyperparasitoidOf" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Hyperparasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002554", + "lbl" : "hyperparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of hyperparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "has epiparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has hyperparasite" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hyperparasitoidized by" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002555", + "lbl" : "allelopath of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Allelopathy" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/allelopathyYes" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002556", + "lbl" : "pathogen of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002557", + "lbl" : "has pathogen", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002558", + "lbl" : "has evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of is evidence for" + }, + "comments" : [ "x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/25052702" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002559", + "lbl" : "causally influenced by", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influenced by (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002560", + "lbl" : "is asymmetric relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002561", + "lbl" : "is symmetric relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002562", + "lbl" : "is relational form of process class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002563", + "lbl" : "interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002564", + "lbl" : "molecular interaction relation helper property", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002565", + "lbl" : "results in movement of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002566", + "lbl" : "causally influences", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "causally influences (entity-centric)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "lbl" : "biomechanically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002568", + "lbl" : "has muscle antagonist", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Antagonist_(muscle)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002569", + "lbl" : "has branching part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of branching part of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002570", + "lbl" : "conduit for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "UBERON:cjm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002571", + "lbl" : "lumen of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:cjm" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002572", + "lbl" : "luminal space of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002573", + "lbl" : "has modifier", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between an attribute or a qualifier and another attribute." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002574", + "lbl" : "participates in a biotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dx.doi.org/10.1016/j.ecoinf.2014.08.005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002575", + "lbl" : "is direct form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The general property hierarchy is:\n\n \"directly P\" SubPropertyOf \"P\"\n Transitive(P)\n\nWhere we have an annotation assertion\n\n \"directly P\" \"is direct form of\" \"P\"" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002423", + "val" : "If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002576", + "lbl" : "skeleton of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has skeleton" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002578", + "lbl" : "directly regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002579", + "lbl" : "is indirect form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002580", + "lbl" : "logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002581", + "lbl" : "is a defining property chain axiom", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002582", + "lbl" : "is a defining property chain axiom where second argument is reflexive", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002583", + "lbl" : "existence starts at end of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002584", + "lbl" : "has part structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002585", + "lbl" : "results in closure of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002586", + "lbl" : "results in breakdown of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002587", + "lbl" : "results in synthesis of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002588", + "lbl" : "results in assembly of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002589", + "lbl" : "results in catabolism of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002590", + "lbl" : "results in disassembly of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002591", + "lbl" : "results in remodeling of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002592", + "lbl" : "results in organization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002593", + "lbl" : "existence ends at start of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002594", + "lbl" : "is relational form of a class", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002595", + "lbl" : "causal relation between material entity and a process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002596", + "lbl" : "capable of regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pyrethroid -> growth" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002597", + "lbl" : "capable of negatively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002598", + "lbl" : "capable of positively regulating", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "renin -> arteriolar smooth muscle contraction" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002599", + "lbl" : "capable of inhibiting or preventing pathological process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "pazopanib -> pathological angiogenesis" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002600", + "lbl" : "capable of upregulating or causing pathological process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "benzene -> cancer [CHEBI]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "causes disease" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002601", + "lbl" : "logical macro assertion involving identity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A shortcut relationship that holds between two entities based on their identity criteria" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002602", + "lbl" : "in approximate one to one relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002603", + "lbl" : "is approximately equivalent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, \"Database D states that x=y\"" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002604", + "lbl" : "is opposite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'anterior end of organism' is-opposite-of 'posterior end of organism'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'increase in temperature' is-opposite-of 'decrease in temperature'" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002605", + "lbl" : "is indistinguishable from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002606", + "lbl" : "is substance that treats", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "treats" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://code.google.com/p/obo-relations/issues/detail?id=46" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002607", + "lbl" : "is marker for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "May be ceded to OBI" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002608", + "lbl" : "process has causal agent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'causal agent in process'" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002609", + "lbl" : "obsolete related via dependence to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002610", + "lbl" : "correlated with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Groups both positive and negative correlation" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002611", + "lbl" : "evidential logical macro assertion on an axiom", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002612", + "lbl" : "axiom has evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002613", + "lbl" : "axiom contradicted by evidence", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002614", + "lbl" : "is evidence with support from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a piece of evidence and an entity that plays a role in supporting that evidence." + }, + "comments" : [ "In the Gene Ontology association model, this corresponds to the With/From field" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002615", + "lbl" : "has model", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of is-model-of" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002616", + "lbl" : "related via evidence or inference to", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002617", + "lbl" : "is representative IRI for equivalence set", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this property relates an IRI to the xsd boolean value \"True\" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002618", + "lbl" : "visits", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/74" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002619", + "lbl" : "visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002622", + "lbl" : "visits flowers of", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002623", + "lbl" : "has flowers visited by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002624", + "lbl" : "lays eggs in", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002625", + "lbl" : "has eggs laid in by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002626", + "lbl" : "kills", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://github.com/jhpoelen/eol-globi-data/issues/143" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002627", + "lbl" : "is killed by", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002629", + "lbl" : "directly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002630", + "lbl" : "directly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002578" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002632", + "lbl" : "ectoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002633", + "lbl" : "has ectoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ectoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002634", + "lbl" : "endoparasite of", + "type" : "PROPERTY", + "meta" : { + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "lives inside of" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002635", + "lbl" : "has endoparasite", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002636", + "lbl" : "mesoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002637", + "lbl" : "has mesoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of mesoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002638", + "lbl" : "intercellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002639", + "lbl" : "has intercellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intercellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002640", + "lbl" : "intracellular endoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of endoparasite-of in which the parasite inhabits host cells." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Parasitism#Types" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002641", + "lbl" : "has intracellular endoparasite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of intracellular endoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002801", + "lbl" : "co-roosts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Communal_roosting" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003000", + "lbl" : "produces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." + }, + "comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "lbl" : "produced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a produced_by b iff some process that occurs_in b has_output a." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003002", + "lbl" : "represses expression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003003", + "lbl" : "increases expression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003301", + "lbl" : "has role in modeling", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity." + }, + "comments" : [ "The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-1048-5019" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is used to study" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003302", + "lbl" : "causes or contributes to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition." + }, + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to.\n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'.\n\nAn environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003303", + "lbl" : "causes condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003304", + "lbl" : "contributes to condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003305", + "lbl" : "contributes to severity of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to expressivity of condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003306", + "lbl" : "contributes to frequency of condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "contributes to penetrance of condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003307", + "lbl" : "ameliorates condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition." + }, + "comments" : [ "Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. \n\nEnvironmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preventative for condition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003308", + "lbl" : "correlated with condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003309", + "lbl" : "exacerbates condition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003310", + "lbl" : "condition ameliorated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0003311", + "lbl" : "condition exacerbated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004000", + "lbl" : "condition has genetic basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:38:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004001", + "lbl" : "has material basis in gain of function germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:20Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410295" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_410296" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004002", + "lbl" : "has material basis in loss of function germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:37Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004003", + "lbl" : "has material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:45:54Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004004", + "lbl" : "has material basis in somatic mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:07Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004005", + "lbl" : "has major susceptibility factor", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:26Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004006", + "lbl" : "has partial material basis in germline mutation in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:46:57Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004007", + "lbl" : "has primary input or output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:17Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004008", + "lbl" : "has primary output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.", + "xrefs" : [ "GOC:kva", "GOC:pt", "GOC:cjm", "GOC:dph" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004009", + "lbl" : "has primary input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.", + "xrefs" : [ "GOC:kva", "GOC:pt", "GOC:cjm", "GOC:dph" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-12-13T11:26:56Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004010", + "lbl" : "is genetic basis for condition", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a more specific relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:53:08Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004011", + "lbl" : "is causal gain of function germline mutation of in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : 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"http://purl.obolibrary.org/obo/RO_0004013", + "lbl" : "is causal germline mutation in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:56:40Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317343" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004014", + "lbl" : "is causal somatic mutation in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T02:57:07Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.orpha.net/ORDO/Orphanet_317344" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004015", + "lbl" : "is causal susceptibility factor for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + 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"http://purl.obolibrary.org/obo/RO_0004017", + "lbl" : "realizable has basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:01Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004018", + "lbl" : "is basis for realizable", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:20:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004019", + "lbl" : "disease has basis in", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:26:47Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004020", + "lbl" : "disease has basis in dysfunction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in dysfunction of (disease to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:29:32Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004021", + "lbl" : "disease has basis in disruption of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease has basis in disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:37:52Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004022", + "lbl" : "disease has basis in feature", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between the disease and a feature (a phenotype or other disease) where the 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It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:50:54Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004024", + "lbl" : "disease causes disruption of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and a process where the disease process disrupts the execution of the process." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes disruption of (disease to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:51:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004025", + "lbl" : "disease causes dysfunction of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "disease causes dysfunction of (disease to anatomical entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T03:58:20Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004026", + "lbl" : "disease has location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: complete range axiom once more of CARO has been mireoted in to this ontology" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-11-05T04:06:02Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004027", + "lbl" : "disease has inflammation site", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:37:31Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004028", + "lbl" : "realized in response to stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:45:49Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004029", + "lbl" : "disease has feature", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:50:53Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004030", + "lbl" : "disease arises from alteration in structure", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-26T19:58:44Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004031", + "lbl" : "enables subfunction", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-25T23:20:13Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004032", + "lbl" : "acts upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:30Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004033", + "lbl" : "acts upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002264" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:49:51Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004034", + "lbl" : "acts upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004035", + "lbl" : "acts upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-01-26T23:53:22Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004036", + "lbl" : "nominally disjoint with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004046", + "lbl" : "causally upstream of or within, negative effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:05Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004047", + "lbl" : "causally upstream of or within, positive effect", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002418" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:55:19Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004048", + "lbl" : "is directional form of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be \"+\", \"-\" or \"0\"" + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-13T23:59:29Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004049", + "lbl" : "is positive form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:16Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007000", + "lbl" : "has driver", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0007001", + "lbl" : "has disease driver", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-8910-9851" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/506" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008501", + "lbl" : "epiphyte of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Epiphyte" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008502", + "lbl" : "has epiphyte", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of epiphyte of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008503", + "lbl" : "kleptoparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Kleptoparasitism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008504", + "lbl" : "kleptoparasitized by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of kleptoparasite of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008505", + "lbl" : "creates habitat for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008506", + "lbl" : "ecologically co-occurs with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship describing organisms that often occur together at the same time and space or in the same environment." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008507", + "lbl" : "lays eggs on", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0008508", + "lbl" : "has eggs laid on by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of lays eggs on" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009001", + "lbl" : "has substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "muffin 'has substance added' some 'baking soda'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009002", + "lbl" : "has substance removed", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'egg white' 'has substance removed' some 'egg yolk'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009003", + "lbl" : "immersed in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardines 'immersed in' some 'oil and mustard'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009004", + "lbl" : "has consumer", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "sardine has consumer some homo sapiens" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009005", + "lbl" : "has primary substance added", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bread 'has primary substance added' some 'flour'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-8844-9165" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0009501", + "lbl" : "realized in response to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "triggered by process", + "xrefs" : [ "RO:cjm" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : 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"receives synaptic input throughout", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:55:36Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013006", + "lbl" : "sends synaptic output throughout", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion)." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:57:27Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013007", + "lbl" : "has sensory dendrite in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has sensory dendrite location" + }, { + "pred" : "hasExactSynonym", + "val" : "has sensory terminal in" + }, { + "pred" : "hasExactSynonym", + "val" : "has sensory terminal location" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-20T12:10:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013008", + "lbl" : "receives synaptic input from neuron", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-05-26T08:40:18Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0013009", + "lbl" : "sends synaptic output to cell", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to." + }, + "comments" : [ "Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron." ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-1373-1705" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-05-26T08:41:07Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0014001", + "lbl" : "disease has infectious agent", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0001-5208-3432" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015001", + "lbl" : "has exemplar data", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and some data in which the data is taken as exemplifying the material entity." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data])" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-5260-9315" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is not meant to capture the relation between occurrents and data." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015002", + "lbl" : "exemplar data of", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-5260-9315" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015003", + "lbl" : "subcluster of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a group and another group it is part of but does not fully constitute." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7258-9596" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015004", + "lbl" : "has characterizing marker set", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has marker gene combination" + }, { + "pred" : "hasExactSynonym", + "val" : "has marker signature set" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1')." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context." + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0001-7258-9596" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015006", + "lbl" : "different in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015007", + "lbl" : "increased in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "lbl" : "decreased in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015009", + "lbl" : "similar in magnitude relative to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "lbl" : "has relative magnitude", + "type" : "PROPERTY" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015011", + "lbl" : "has cross section", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015012", + "lbl" : "reciprocal of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015015", + "lbl" : "has high plasma membrane amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "lbl" : "has low plasma membrane amount", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "http://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016001", + "lbl" : "has phenotype or disease", + "type" : "PROPERTY", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:14Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016002", + "lbl" : "has disease", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "http://orcid.org/0000-0002-7463-6306" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-11-05T17:30:44Z" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/oborel/obo-relations/issues/478" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0016004", + "lbl" : "has exposure medium", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000083" + }, { + "pred" : "http://purl.org/dc/elements/1.1/date", + "val" : "2021-12-14T20:41:45Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7463-6306" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0017001", + "lbl" : "device utilizes material", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "utilizes" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A diagnostic testing device utilizes a specimen." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-2620-0345" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-11-08T12:00:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018001", + "lbl" : "is myristoyltransferase activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Helper relation for OWL definition of RO:0018002 myristoylates" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018002", + "lbl" : "myristoylates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/conformsTo", + "val" : "http://purl.obolibrary.org/obo/ro/ro-metamodel/ObjectPropertyDefinedByInteractionProcess" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018003", + "lbl" : "myristoylated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of myristoylates" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018027", + "lbl" : "is agonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275)" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "https://orcid.org/0000-0003-4423-4370" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://www.wikidata.org/wiki/Property:P3772" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0018028", + "lbl" : "is inverse agonist of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + 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"http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002380", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002377", "http://purl.obolibrary.org/obo/RO_0002381" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002413", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002402", "http://purl.obolibrary.org/obo/RO_0002400" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002409" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002409", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002403", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002411", "http://purl.obolibrary.org/obo/RO_0002402" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002553", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002444", "http://purl.obolibrary.org/obo/RO_0002444" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002554", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002445", "http://purl.obolibrary.org/obo/RO_0002445" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000062" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/RO_0002082" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/BFO_0000063" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002509", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002507", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002205", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002511", "http://purl.obolibrary.org/obo/RO_0002513" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002204", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002512", "http://purl.obolibrary.org/obo/RO_0002510" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002526", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002524", "http://purl.obolibrary.org/obo/RO_0002525" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002211", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002578", "http://purl.obolibrary.org/obo/RO_0002578" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002583", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002593", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002407" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002629", "http://purl.obolibrary.org/obo/RO_0002629" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002409" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004024", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004025", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004024", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0004025", "http://purl.obolibrary.org/obo/RO_0002215" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004028", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0009501", "http://purl.obolibrary.org/obo/RO_0002233" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013002", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013002", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013003", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013003", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0013007", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013007", "http://purl.obolibrary.org/obo/BFO_0000050" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0015001", + "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0015001", "http://purl.obolibrary.org/obo/RO_0015003" ] + } ] + } ] +} \ No newline at end of file diff --git a/subsets/ro-eco.obo b/subsets/ro-eco.obo index 7f3fab39..1bf9637b 100644 --- a/subsets/ro-eco.obo +++ b/subsets/ro-eco.obo @@ -7,7 +7,6 @@ subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam "" subsetdef: ro-eco "" subsetdef: RO:0002259 "" ontology: ro/subsets/ro-eco -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(DataProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: ()\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (never in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (mutually spatially disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (taxonomic class assertion)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (ambiguous for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dubious for taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (annotation property cardinality)\n\nSubAnnotationPropertyOf( )\nAnnotationPropertyRange( xsd:nonNegativeInteger)\n\n# Annotation Property: (logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on a property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an object property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an annotation property)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (dispositional interpretation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has no connections with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (curator guidance link)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (always present in taxon)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (temporal logical macro assertion on a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (measurement property has unit)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has start time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has end time value)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post fertilization)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, years post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, months post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (month of gestation)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (has developmental stage marker)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, days post coitum)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (start, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (end, weeks post birth)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is asymmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is symmetric relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of process class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is direct form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indirect form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is a defining property chain axiom where second argument is reflexive)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is relational form of a class)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (logical macro assertion involving identity)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (in approximate one to one relationship with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is approximately equivalent to)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is opposite of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is indistinguishable from)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (evidential logical macro assertion on an axiom)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom has evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (axiom contradicted by evidence)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is representative IRI for equivalence set)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (nominally disjoint with)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is directional form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is positive form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is negative form of)\n\nSubAnnotationPropertyOf( )\n\n# Annotation Property: (is homeomorphic for)\n\nSubAnnotationPropertyOf( )\n\n\n############################\n# Object Properties\n############################\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has role in modeling)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance added)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has substance removed)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (immersed in)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (has primary substance added)\n\nIrreflexiveObjectProperty()\n\n\n############################\n# Data Properties\n############################\n\n# Data Property: (has increased age-specific mortality rate)\n\nDataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short))\n\n\n\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: BFO:0000050 @@ -177,7 +176,7 @@ is_a: RO:0001018 ! contained in [Typedef] id: RO:0002005 name: innervated_by -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 xsd:anyURI +property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 inverse_of: RO:0002134 ! innervates @@ -685,7 +684,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -788,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -798,8 +797,8 @@ name: connected to def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -809,8 +808,8 @@ def: "c connects a if and only if there exist some b such that a and b are simil property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -1120,7 +1119,7 @@ is_a: RO:0002220 ! adjacent to [Typedef] id: RO:0002222 subset: ro-eco -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string @@ -1259,28 +1258,28 @@ property_value: IAO:0000232 "This object property is needed for axioms using has id: RO:0002240 name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002241 name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: RO:0002309 ! has exposure stimulus [Typedef] id: RO:0002242 name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: RO:0002244 ! related via exposure to [Typedef] id: RO:0002243 name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: RO:0002244 ! related via exposure to [Typedef] @@ -1370,7 +1369,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string is_a: RO:0002258 ! developmentally preceded by @@ -1492,7 +1491,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1506,7 +1505,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -1522,7 +1521,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1537,7 +1536,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1654,7 +1653,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: RO:0002295 ! results in developmental progression of is_a: RO:0040036 ! results in changes to anatomical or cellular structure @@ -1967,7 +1966,7 @@ is_a: RO:0002295 ! results in developmental progression of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002131 ! overlaps @@ -1987,7 +1986,7 @@ id: RO:0002372 name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -1997,7 +1996,7 @@ id: RO:0002373 name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion is_a: RO:0002371 ! attached to is_a: RO:0002567 ! biomechanically related to @@ -2024,7 +2023,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -2039,11 +2038,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with @@ -2058,7 +2057,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: RO:0002170 ! connected to is_a: RO:0002375 ! in branching relationship with @@ -2090,7 +2089,7 @@ def: "x is a branching part of y if and only if x is part of y and x is connecte subset: ro-eco property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 holds_over_chain: RO:0002377 RO:0002381 is_a: BFO:0000050 @@ -2337,7 +2336,7 @@ name: differs in comment: This is an exploratory relation property_value: IAO:0000116 "false" xsd:boolean property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions xsd:anyURI +property_value: seeAlso "https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions" xsd:anyURI [Typedef] id: RO:0002425 @@ -2427,18 +2426,18 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_symmetric: true [Typedef] id: RO:0002435 name: genetically interacts with -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 @@ -2449,7 +2448,7 @@ is_a: RO:0002434 ! interacts with id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -2465,7 +2464,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string is_symmetric: true is_a: RO:0002321 ! ecologically related to is_a: RO:0002434 ! interacts with @@ -2491,8 +2490,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: RO:0002438 ! trophically interacts with inverse_of: RO:0002458 ! preyed upon by @@ -2502,7 +2501,7 @@ name: symbiotically interacts with def: "A biotic interaction in which the two organisms live together in more or less intimate association." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -2513,7 +2512,7 @@ name: commensually interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -2522,7 +2521,7 @@ name: mutualistically interacts with def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -2531,7 +2530,7 @@ name: interacts with via parasite-host interaction def: "An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO)." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: RO:0002440 ! symbiotically interacts with @@ -2543,7 +2542,7 @@ synonym: "direct parasite of" EXACT [] property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002454 ! has host inverse_of: RO:0002445 ! parasitized by @@ -2556,7 +2555,7 @@ synonym: "directly parasitized by" EXACT [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: RO:0002443 ! interacts with via parasite-host interaction is_a: RO:0002453 ! host of @@ -2639,7 +2638,7 @@ name: has host def: "X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y" [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: RO:0002440 ! symbiotically interacts with [Typedef] @@ -2650,7 +2649,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: RO:0002442 ! mutualistically interacts with inverse_of: RO:0002456 ! pollinated by @@ -2661,7 +2660,7 @@ subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: RO:0002442 ! mutualistically interacts with [Typedef] @@ -2682,8 +2681,8 @@ subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: RO:0002438 ! trophically interacts with [Typedef] @@ -3058,7 +3057,7 @@ id: RO:0002510 name: transcribed from def: "x is transcribed from y if and only if x is synthesized from template y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002511 ! transcribed to @@ -3068,7 +3067,7 @@ name: transcribed to def: "inverse of transcribed from" [] subset: RO:0002259 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to [Typedef] @@ -3076,7 +3075,7 @@ id: RO:0002512 name: ribosomal translation of def: "x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to inverse_of: RO:0002513 ! ribosomally translates to @@ -3085,7 +3084,7 @@ id: RO:0002513 name: ribosomally translates to def: "inverse of ribosomal translation of" [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002330 ! genomically related to [Typedef] @@ -3094,7 +3093,7 @@ name: sequentially related to def: "A relation that holds between two entities that have the property of being sequences or having sequences. " [] property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string @@ -3107,7 +3106,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002527 ! does not overlap sequence of [Typedef] @@ -3118,7 +3117,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002524 ! has subsequence inverse_of: RO:0002517 ! is start sequence of @@ -3131,7 +3130,7 @@ subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002525 ! is subsequence of @@ -3143,7 +3142,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002524 ! has subsequence inverse_of: RO:0002519 ! is end sequence of @@ -3156,7 +3155,7 @@ subset: RO:0002259 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: RO:0002525 ! is subsequence of @@ -3167,7 +3166,7 @@ def: "x is a consecutive sequence of y iff x has subsequence y, and all the part property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: RO:0002524 ! has subsequence [Typedef] @@ -3208,7 +3207,7 @@ def: "x has subsequence y iff all of the sequence parts of y are sequence parts property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: BFO:0000051 is_a: RO:0002522 ! bounds sequence of @@ -3318,8 +3317,8 @@ synonym: "epiparasite of" RELATED [] synonym: "hyperparasitoid of" NARROW [] property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string holds_over_chain: RO:0002444 RO:0002444 is_a: RO:0002454 ! has host inverse_of: RO:0002554 ! hyperparasitized by @@ -3342,8 +3341,8 @@ id: RO:0002555 name: allelopath of subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with @@ -3387,7 +3386,7 @@ id: RO:0002563 name: interaction relation helper property property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] @@ -3430,7 +3429,7 @@ id: RO:0002568 name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: RO:0002567 ! biomechanically related to [Typedef] @@ -3450,7 +3449,7 @@ name: conduit for def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string is_a: RO:0002131 ! overlaps @@ -3460,7 +3459,7 @@ name: lumen of def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] subset: ro-eco property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string is_a: BFO:0000050 [Typedef] @@ -3695,7 +3694,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is a grouping [Typedef] id: RO:0002618 name: visits -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002619 ! visited by @@ -3731,7 +3730,7 @@ is_a: RO:0002619 ! visited by [Typedef] id: RO:0002626 name: kills -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: RO:0002574 ! participates in a biotic-biotic interaction with inverse_of: RO:0002627 ! is killed by @@ -3770,7 +3769,7 @@ is_a: RO:0002578 ! directly regulates id: RO:0002632 name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002444 ! parasite of inverse_of: RO:0002633 ! has ectoparasite @@ -3786,7 +3785,7 @@ id: RO:0002634 name: endoparasite of synonym: "lives inside of" RELATED [] property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002444 ! parasite of inverse_of: RO:0002635 ! has endoparasite @@ -3813,7 +3812,7 @@ is_a: RO:0002445 ! parasitized by id: RO:0002638 name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002639 ! has intercellular endoparasite @@ -3828,7 +3827,7 @@ is_a: RO:0002635 ! has endoparasite id: RO:0002640 name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: RO:0002634 ! endoparasite of inverse_of: RO:0002641 ! has intracellular endoparasite @@ -4322,7 +4321,7 @@ is_a: RO:0007000 ! has driver id: RO:0008501 name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: RO:0002440 ! symbiotically interacts with inverse_of: RO:0008502 ! has epiphyte @@ -4337,7 +4336,7 @@ is_a: RO:0002440 ! symbiotically interacts with id: RO:0008503 name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: RO:0002444 ! parasite of inverse_of: RO:0008504 ! kleptoparasitized by @@ -4428,7 +4427,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI is_a: RO:0002410 ! causally related to [Typedef] @@ -4872,25 +4871,25 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0016001 name: has phenotype or disease property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: RO:0016002 name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: RO:0016001 ! has phenotype or disease [Typedef] id: RO:0016004 name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: RO:0002244 ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 diff --git a/subsets/ro-eco.tsv b/subsets/ro-eco.tsv new file mode 100644 index 00000000..e69de29b diff --git a/subsets/ro-hom.json b/subsets/ro-hom.json new file mode 100644 index 00000000..ade7fe10 --- /dev/null +++ b/subsets/ro-hom.json @@ -0,0 +1,2808 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-hom.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/RO_0002156", + "lbl" : "derived by descent from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." + }, + "xrefs" : [ { + "val" : "RO:0002156" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ancestral_stucture_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "evolutionarily_descended_from" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "derived_by_descent_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002157", + "lbl" : "has derived by descendant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of derived by descent from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002157" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_derived_by_descendant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ], + "xrefs" : [ { + "val" : "RO:0002158" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "shares_ancestor_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002159", + "lbl" : "serially homologous to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002159" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "serially_homologous_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." + }, + "xrefs" : [ { + "val" : "RO:0002160" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "only_in_taxon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + }, + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002162" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9227-417X" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_taxon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002312", + "lbl" : "evolutionary variant of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002312" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "evolutionary_variant_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some environmental process" + }, + "xrefs" : [ { + "val" : "RO:0002320" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "evolutionarily_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002374", + "lbl" : "derived from ancestral fusion of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" + }, + "comments" : [ "A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B." ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "has fused element" + } ], + "xrefs" : [ { + "val" : "RO:0002374" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "derived_from_ancestral_fusion_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000000", + "lbl" : "in similarity relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.", + "xrefs" : [ "http://purl.obolibrary.org/obo/HOM_0000000", "BGEE:curator" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "sameness" + }, { + "pred" : "hasExactSynonym", + "val" : "similar to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "correspondence", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814479" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "resemblance" + } ], + "xrefs" : [ { + "val" : "ECO:0000041" + }, { + "val" : "SO:similar_to" + }, { + "val" : "RO:HOM0000000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO: Add homeomorphy axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_similarity_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000000" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000001", + "lbl" : "in homology relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Similarity that results from common evolutionary origin.", + "xrefs" : [ "http://dx.doi.org/10.1002/bies.950180611", "http://dx.doi.org/10.1002/jmor.1051730307", "http://dx.doi.org/10.1007/BF02814480", "http://purl.obolibrary.org/obo/HOM_0000001" ] + }, + "comments" : [ "This broad definition encompasses all the working definitions proposed so far in the literature." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homologous to" + } ], + "xrefs" : [ { + "val" : "RO:HOM0000001" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_homology_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000001" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000002", + "lbl" : "in homoplasy relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Similarity that results from independent evolution.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000002" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homoplasous to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "analogy" + } ], + "xrefs" : [ { + "val" : "RO:HOM0000002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_homoplasy_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000002" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000003", + "lbl" : "in homocracy relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes.", + "xrefs" : [ "http://dx.doi.org/10.1007/BF02814484", "http://dx.doi.org/10.1007/s00427-003-0301-4", "http://dx.doi.org/10.1186/1742-9994-2-15", "http://purl.obolibrary.org/obo/HOM_0000003" ] + }, + "comments" : [ "Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "homocracous to" + } ], + "xrefs" : [ { + "val" : "ECO:0000075" + }, { + "val" : "RO:HOM0000003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_homocracy_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000003" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000004", + "lbl" : "in convergence relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Homoplasy that involves different underlying mechanisms or structures.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000004" ] + }, + "comments" : [ "Convergence usually implies a notion of adaptation." ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "analogy" + } ], + "xrefs" : [ { + "val" : "RO:HOM0000004" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_convergence_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000004" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000005", + "lbl" : "in parallelism relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Homoplasy that involves homologous underlying mechanisms or structures.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.010", "http://purl.obolibrary.org/obo/HOM_0000005" ] + }, + "comments" : [ "Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "parallel evolution" + } ], + "xrefs" : [ { + "val" : "RO:HOM0000005" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_parallelism_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000005" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000006", + "lbl" : "in structural homology relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Homology that is defined by similarity with regard to selected structural parameters.", + "xrefs" : [ "http://dx.doi.org/10.1016/j.jhevol.2006.11.014", "http://dx.doi.org/10.1146/annurev.es.20.110189.000411", "http://purl.obolibrary.org/obo/HOM_0000006", "ISBN:0123195837" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "structural homologous to" + }, { + "pred" : "hasRelatedSynonym", + "val" : "idealistic homology" + } ], + "xrefs" : [ { + "val" : "ECO:0000071" + }, { + "val" : "MI:2163" + }, { + "val" : "RO:HOM0000006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/elements/1.1/creator", + "val" : "http://bgee.unil.ch" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20116127" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_structural_homology_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/HOM_0000006" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_HOM0000007", + "lbl" : "in historical homology relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Homology that is defined by common descent.", + "xrefs" : [ "http://dx.doi.org/10.1016/S0169-5347(97)01125-7", "http://purl.obolibrary.org/obo/HOM_0000007", "ISBN:0123195837" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "homology" + }, { + "pred" : "hasExactSynonym", + "val" : "cladistic homology" + }, { + "pred" : "hasExactSynonym", + "val" : "historical homologous to" + }, { + "pred" : "hasExactSynonym", + "val" : "phylogenetic homology" + }, { + "pred" : "hasExactSynonym", + "val" : "taxic homology" + }, { + "pred" : "hasRelatedSynonym", + 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"http://purl.obolibrary.org/obo/RO_HOM0000043", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000044", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000044", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000005" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000045", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000046", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000047" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000047", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000048", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000048", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000036" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000049", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000050", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000051", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000029" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000052", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000053", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000018" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000054", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000017" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000054", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000062" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000055", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000057", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000005" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000057", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000058" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000058", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000060", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000019" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000060", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000050" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000061", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000018" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000062", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000062", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000065" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000063", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000065", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000066", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000008" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000068", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000018" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000069", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000071", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000006" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000072", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000008" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000073", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000022" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000073", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000053" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000074", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000003" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000074", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000066" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_HOM0000075", + "pred" : "subPropertyOf", + "obj" : "http://purl.obolibrary.org/obo/RO_HOM0000007" + }, { + "sub" : "http://purl.obolibrary.org/obo/RO_0002156", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/RO_0002157" + } ], + "domainRangeAxioms" : [ { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0001010" ] + } ] + } ] +} \ No newline at end of file diff --git a/subsets/ro-hom.obo b/subsets/ro-hom.obo index 301fb31e..27d2a0be 100644 --- a/subsets/ro-hom.obo +++ b/subsets/ro-hom.obo @@ -1,10 +1,1018 @@ format-version: 1.2 ontology: ro/subsets/ro-hom +[Typedef] +id: derived_by_descent_from +name: derived by descent from +def: "d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a." [] +xref: RO:0002156 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000118 "ancestral_stucture_of" xsd:string +property_value: IAO:0000118 "evolutionarily_descended_from" xsd:string +is_transitive: true +is_a: evolutionarily_related_to ! evolutionarily related to +inverse_of: has_derived_by_descendant ! has derived by descendant + +[Typedef] +id: derived_from_ancestral_fusion_of +name: derived from ancestral fusion of +def: "x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat" [] +comment: A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. +synonym: "has fused element" BROAD [] +xref: RO:0002374 +property_value: IAO:0000112 "false" xsd:boolean +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 +is_a: derived_by_descent_from ! derived by descent from + +[Typedef] +id: evolutionarily_related_to +name: evolutionarily related to +def: "A relationship that holds via some environmental process" [] +xref: RO:0002320 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string + +[Typedef] +id: evolutionary_variant_of +name: evolutionary variant of +xref: RO:0002312 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: evolutionarily_related_to ! evolutionarily related to + +[Typedef] +id: has_derived_by_descendant +name: has derived by descendant +def: "inverse of derived by descent from" [] +subset: RO:0002259 +xref: RO:0002157 +property_value: IAO:0000114 IAO:0000125 +is_transitive: true +is_a: evolutionarily_related_to ! evolutionarily related to + +[Typedef] +id: in_1_to_1_homology_relationship_with +name: in 1 to 1 homology relationship with +def: "Historical homology that involves two members sharing no other homologs in the lineages considered." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000019] +synonym: "1 to 1 homologous to" EXACT [] +synonym: "1:1 homology" EXACT [] +synonym: "one-to-one homology" EXACT [] +xref: RO:HOM0000019 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000019 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_1_to_1_orthology_relationship_with +name: in 1 to 1 orthology relationship with +def: "Orthology that involves two genes that did not experience any duplication after the speciation event that created them." [http://dx.doi.org/10.1007/BF02814484, http://purl.obolibrary.org/obo/HOM_0000020, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "1 to 1 orthologous to" EXACT [] +synonym: "1:1 orthology" EXACT [] +synonym: "one-to-one orthology" EXACT [] +xref: RO:HOM0000020 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000020 +is_symmetric: true +is_a: in_1_to_1_homology_relationship_with ! in 1 to 1 homology relationship with +is_a: in_orthology_relationship_with ! in orthology relationship with + +[Typedef] +id: in_1_to_many_homology_relationship_with +name: in 1 to many homology relationship with +def: "Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000037] +synonym: "1 to many homologous to" EXACT [] +synonym: "1:many homology" RELATED [] +synonym: "one-to-many homology" EXACT [] +xref: RO:HOM0000037 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000037 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_1_to_many_orthology_relationship_with +name: in 1 to many orthology relationship with +def: "Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000034, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "1 to many orthologous to" EXACT [] +synonym: "1:many orthology" EXACT [] +synonym: "co-orthology" RELATED [] +synonym: "many to 1 orthology" RELATED [] +synonym: "one-to-many orthology" EXACT [] +xref: RO:HOM0000034 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000034 +is_symmetric: true +is_a: in_1_to_many_homology_relationship_with ! in 1 to many homology relationship with +is_a: in_orthology_relationship_with ! in orthology relationship with + +[Typedef] +id: in_apomorphy_relationship_with +name: in apomorphy relationship with +def: "Historical homology that is based on recent shared ancestry, characterizing a monophyletic group." [http://purl.obolibrary.org/obo/HOM_0000042, ISBN:978-0252068140] +synonym: "apomorphous to" EXACT [] +synonym: "synapomorphy" RELATED [] +xref: RO:HOM0000042 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000042 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with +disjoint_from: in_plesiomorphy_relationship_with ! in plesiomorphy relationship with + +[Typedef] +id: in_apparent_orthology_relationship_with +name: in apparent orthology relationship with +def: "Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000060, http://www.ensembl.org/info/docs/compara/homology_method.html] +comment: The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. +synonym: "1:1 paralogy" EXACT [] +synonym: "apparent 1:1 orthology" EXACT [] +synonym: "apparent orthologous to" EXACT [] +synonym: "pseudoorthology" EXACT [] +xref: RO:HOM0000060 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000060 +is_symmetric: true +is_a: in_1_to_1_homology_relationship_with ! in 1 to 1 homology relationship with +is_a: in_between-species_paralogy_relationship_with ! in between-species paralogy relationship with + +[Typedef] +id: in_between-species_paralogy_relationship_with +name: in between-species paralogy relationship with +def: "Paralogy that involves genes from different species." [http://purl.obolibrary.org/obo/HOM_0000050, http://www.ensembl.org/info/docs/compara/homology_method.html] +comment: The genes have diverged before a speciation event. +synonym: "between-species paralogous to" EXACT [] +xref: RO:HOM0000050 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000050 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with + +[Typedef] +id: in_biological_homology_relationship_with +name: in biological homology relationship with +def: "Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000008] +comment: Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. +synonym: "biological homologous to" EXACT [] +synonym: "transformational homology" RELATED [] +xref: ECO:0000067 +xref: RO:HOM0000008 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000008 +is_symmetric: true +is_a: in_homology_relationship_with ! in homology relationship with + +[Typedef] +id: in_chromosomal_homology_relationship_with +name: in chromosomal homology relationship with +def: "Historical homology that involves the chromosomes able to pair (synapse) during meiosis." [http://purl.obolibrary.org/obo/HOM_0000047, ISBN:0195307615] +synonym: "chromosomal homologous to" EXACT [] +xref: MeSH:Chromosome_Pairing +xref: RO:HOM0000047 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000047 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_convergence_relationship_with +name: in convergence relationship with +def: "Homoplasy that involves different underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000004] +comment: Convergence usually implies a notion of adaptation. +synonym: "analogy" RELATED [] +xref: RO:HOM0000004 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000004 +is_symmetric: true +is_a: in_homoplasy_relationship_with ! in homoplasy relationship with + +[Typedef] +id: in_deep_homology_relationship_with +name: in deep homology relationship with +def: "Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1038/nature07891, http://purl.obolibrary.org/obo/HOM_0000044] +comment: Used for structures in distantly related taxa. +synonym: "deep genetic homology" EXACT [] +synonym: "deep homologous to" EXACT [] +synonym: "generative homology" RELATED [] +synonym: "homoiology" RELATED [] +xref: RO:HOM0000044 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000044 +is_symmetric: true +is_a: in_homocracy_relationship_with ! in homocracy relationship with +is_a: in_parallelism_relationship_with ! in parallelism relationship with + +[Typedef] +id: in_equivalogy_relationship_with +name: in equivalogy relationship with +def: "Historical homology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1093/nar/gkl1043, http://purl.obolibrary.org/obo/HOM_0000062] +comment: This may include examples of orthology, paralogy and xenology. +synonym: "equivalogous to" EXACT [] +xref: RO:HOM0000062 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000062 +is_symmetric: true +is_a: in_functional_equivalence_relationship_with ! in functional equivalence relationship with +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_functional_equivalence_relationship_with +name: in functional equivalence relationship with +def: "Similarity that is characterized by interchangeability in function." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000065] +synonym: "functional similarity" RELATED [] +xref: RO:HOM0000065 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000065 +is_symmetric: true +is_a: in_similarity_relationship_with ! in similarity relationship with + +[Typedef] +id: in_gametology_relationship_with +name: in gametology relationship with +def: "Historical homology that involves not recombining and subsequently differentiated sex chromosomes." [http://purl.obolibrary.org/obo/HOM_0000046, http://www.ncbi.nlm.nih.gov/pubmed/11110898] +synonym: "gametologous to" EXACT [] +xref: RO:HOM0000046 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000046 +is_symmetric: true +is_a: in_chromosomal_homology_relationship_with ! in chromosomal homology relationship with + +[Typedef] +id: in_hemiplasy_relationship_with +name: in hemiplasy relationship with +def: "Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree." [http://dx.doi.org/10.1073/pnas.0807433105, http://purl.obolibrary.org/obo/HOM_0000045] +synonym: "hemiplasous to" EXACT [] +xref: RO:HOM0000045 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000045 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_heterochronous_homology_relationship_with +name: in heterochronous homology relationship with +def: "Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures." [http://purl.obolibrary.org/obo/HOM_0000028, ISBN:978-0674639416] +synonym: "heterochronous homologous to" EXACT [] +synonym: "heterochrony" EXACT [] +xref: RO:HOM0000028 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000028 +is_symmetric: true +is_a: in_biological_homology_relationship_with ! in biological homology relationship with + +[Typedef] +id: in_historical_homology_relationship_with +name: in historical homology relationship with +def: "Homology that is defined by common descent." [http://dx.doi.org/10.1016/S0169-5347(97)01125-7, http://purl.obolibrary.org/obo/HOM_0000007, ISBN:0123195837] +synonym: "cladistic homology" EXACT [] +synonym: "historical homologous to" EXACT [] +synonym: "homology" BROAD [] +synonym: "phylogenetic homology" EXACT [] +synonym: "taxic homology" EXACT [] +synonym: "true homology" RELATED [] +xref: ECO:0000080 +xref: RO:HOM0000007 +xref: RO_proposed_relation:homologous_to +xref: SO:0000330 +xref: SO:0000853 +xref: SO:0000857 +xref: SO:homologous_to +xref: TAO:homologous_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000007 +is_symmetric: true +is_a: in_homology_relationship_with ! in homology relationship with + +[Typedef] +id: in_homeosis_relationship_with +name: in homeosis relationship with +def: "Biological homology that involves an ectopic structure and the normally positioned structure." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.cell.2008.06.030, http://purl.obolibrary.org/obo/HOM_0000072] +synonym: "heterotopy" RELATED [] +xref: RO:HOM0000072 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000072 +is_symmetric: true +is_a: in_biological_homology_relationship_with ! in biological homology relationship with + +[Typedef] +id: in_homocracy_relationship_with +name: in homocracy relationship with +def: "Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/s00427-003-0301-4, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000003] +comment: Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. +synonym: "homocracous to" EXACT [] +xref: ECO:0000075 +xref: RO:HOM0000003 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000003 +is_symmetric: true +is_a: evolutionarily_related_to ! evolutionarily related to +is_a: in_similarity_relationship_with ! in similarity relationship with + +[Typedef] +id: in_homoeology_relationship_with +name: in homoeology relationship with +def: "Synology that results from allopolyploidy." [http://dx.doi.org/10.1073/pnas.0505156102, http://purl.obolibrary.org/obo/HOM_0000073] +comment: On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. +synonym: "homoeologous to" EXACT [] +xref: RO:HOM0000073 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000073 +is_symmetric: true +is_a: in_ohnology_relationship_with ! in ohnology relationship with +is_a: in_synology_relationship_with ! in synology relationship with + +[Typedef] +id: in_homology_relationship_with +name: in homology relationship with +def: "Similarity that results from common evolutionary origin." [http://dx.doi.org/10.1002/bies.950180611, http://dx.doi.org/10.1002/jmor.1051730307, http://dx.doi.org/10.1007/BF02814480, http://purl.obolibrary.org/obo/HOM_0000001] +comment: This broad definition encompasses all the working definitions proposed so far in the literature. +synonym: "homologous to" EXACT [] +xref: RO:HOM0000001 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000001 +is_symmetric: true +is_a: in_similarity_relationship_with ! in similarity relationship with +is_a: shares_ancestor_with ! shares ancestor with +disjoint_from: in_homoplasy_relationship_with ! in homoplasy relationship with + +[Typedef] +id: in_homoplasy_relationship_with +name: in homoplasy relationship with +def: "Similarity that results from independent evolution." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000002] +synonym: "analogy" RELATED [] +synonym: "homoplasous to" EXACT [] +xref: RO:HOM0000002 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000002 +is_symmetric: true +is_a: in_similarity_relationship_with ! in similarity relationship with + +[Typedef] +id: in_homotopy_relationship_with +name: in homotopy relationship with +def: "Structural homology that involves structures with the same or similar relative positions." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1007/BF02814485, http://purl.obolibrary.org/obo/HOM_0000071, ISBN:0123195837] +comment: Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. +synonym: "homotopous to" EXACT [] +xref: RO:HOM0000071 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000071 +is_symmetric: true +is_a: in_structural_homology_relationship_with ! in structural homology relationship with +disjoint_from: in_homeosis_relationship_with ! in homeosis relationship with + +[Typedef] +id: in_hypermorphosis_relationship_with +name: in hypermorphosis relationship with +def: "Peramorphosis that is produced by a delay in the offset of development." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000052, ISBN:978-0674639416] +xref: RO:HOM0000052 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000052 +is_symmetric: true +is_a: in_peramorphosis_relationship_with ! in peramorphosis relationship with + +[Typedef] +id: in_in-paralogy_relationship_with +name: in in-paralogy relationship with +def: "Paralogy that results from a lineage-specific duplication subsequent to a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000023] +synonym: "in-paralogous to" EXACT [] +synonym: "inparalogy" EXACT [] +synonym: "symparalogy" EXACT [] +xref: RO:HOM0000023 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000023 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with +disjoint_from: in_out-paralogy_relationship_with ! in out-paralogy relationship with + +[Typedef] +id: in_interology_relationship_with +name: in interology relationship with +def: "Historical homology that involves orthologous pairs of interacting molecules in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://dx.doi.org/10.1126/science.287.5450.116, http://purl.obolibrary.org/obo/HOM_0000063] +synonym: "interologous to" EXACT [] +xref: RO:HOM0000063 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000063 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_isoorthology_relationship_with +name: in isoorthology relationship with +def: "Orthology that involves functional equivalent genes with retention of the ancestral function." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000054] +synonym: "isoorthologous to" EXACT [] +xref: ECO:0000080 +xref: RO:HOM0000054 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000054 +is_symmetric: true +is_a: in_equivalogy_relationship_with ! in equivalogy relationship with +is_a: in_orthology_relationship_with ! in orthology relationship with + +[Typedef] +id: in_iterative_homology_relationship_with +name: in iterative homology relationship with +def: "Biological homology that involves parts of the same organism." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000066] +synonym: "iterative homologous to" EXACT [] +xref: RO:HOM0000066 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000066 +is_symmetric: true +is_a: in_biological_homology_relationship_with ! in biological homology relationship with + +[Typedef] +id: in_latent_homology_relationship_with +name: in latent homology relationship with +def: "Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character)." [http://dx.doi.org/10.1007/BF02814485, http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000057, ISBN:0199141118] +comment: Used for structures in closely related taxa. +synonym: "apomorphic tendency" EXACT [] +synonym: "cryptic homology" EXACT [] +synonym: "homoiology" RELATED [] +synonym: "homoplastic tendency" RELATED [] +synonym: "latent homologous to" EXACT [] +synonym: "re-awakening" RELATED [] +synonym: "underlying synapomorphy" EXACT [] +xref: RO:HOM0000057 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000057 +is_symmetric: true +is_a: in_parallelism_relationship_with ! in parallelism relationship with +is_a: in_syngeny_relationship_with ! in syngeny relationship with + +[Typedef] +id: in_many_to_many_homology_relationship_with +name: in many to many homology relationship with +def: "Historical homology that involves two members of a larger set of homologs." [http://dx.doi.org/10.1093/molbev/msp002, http://purl.obolibrary.org/obo/HOM_0000036] +synonym: "many to many homologous to" EXACT [] +synonym: "many-to-many homology" EXACT [] +synonym: "many:many homology " EXACT [] +xref: RO:HOM0000036 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000036 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_many_to_many_orthology_relationship_with +name: in many to many orthology relationship with +def: "Orthology that involves two genes that experienced duplications more recent than the species split that created them." [http://dx.doi.org/10.1038/415741a, http://purl.obolibrary.org/obo/HOM_0000048, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "co-orthology" RELATED [] +synonym: "many to many orthologous to" EXACT [] +synonym: "many-to-many orthology" EXACT [] +synonym: "many:many orthology" EXACT [] +synonym: "trans-homology" RELATED [] +synonym: "trans-orthology" EXACT [] +xref: RO:HOM0000048 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000048 +is_symmetric: true +is_a: in_many_to_many_homology_relationship_with ! in many to many homology relationship with +is_a: in_orthology_relationship_with ! in orthology relationship with + +[Typedef] +id: in_mimicry_relationship_with +name: in mimicry relationship with +def: "Convergence that results from co-evolution usually involving an evolutionary arms race." [http://en.wikipedia.org/wiki/Mimicry, http://purl.obolibrary.org/obo/HOM_0000033] +synonym: "mimicrous to" EXACT [] +xref: RO:HOM0000033 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000033 +is_symmetric: true +is_a: in_convergence_relationship_with ! in convergence relationship with + +[Typedef] +id: in_neoteny_relationship_with +name: in neoteny relationship with +def: "Paedomorphosis that is produced by a retardation of somatic development." [http://en.wikipedia.org/wiki/Neoteny, http://purl.obolibrary.org/obo/HOM_0000032, ISBN:978-0674639416] +synonym: "juvenilization" EXACT [] +synonym: "neotenous to" EXACT [] +xref: RO:HOM0000032 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000032 +is_symmetric: true +is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with + +[Typedef] +id: in_non_functional_homology_relationship_with +name: in non functional homology relationship with +def: "Structural homology that involves a pseudogenic feature and its functional ancestor." [http://purl.obolibrary.org/obo/HOM_0000016, SO:non_functional_homolog_of] +synonym: "non functional homologous to" EXACT [] +synonym: "pseudogene" BROAD [] +xref: RO:HOM0000016 +xref: SO:non_functional_homolog_of +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000016 +is_symmetric: true +is_a: in_structural_homology_relationship_with ! in structural homology relationship with +disjoint_from: in_equivalogy_relationship_with ! in equivalogy relationship with + +[Typedef] +id: in_ohnology_relationship_with +name: in ohnology relationship with +def: "Paralogy that results from a whole genome duplication event." [http://dx.doi.org/10.1038/75560, http://purl.obolibrary.org/obo/HOM_0000022] +synonym: "homoeology" RELATED [] +synonym: "ohnologous to" EXACT [] +xref: RO:HOM0000022 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000022 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with + +[Typedef] +id: in_orthology_relationship_with +name: in orthology relationship with +def: "Historical homology that involves genes that diverged after a speciation event." [http://dx.doi.org/10.1007/BF02814484, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000017, http://www.ncbi.nlm.nih.gov/pubmed/5449325] +comment: The term is sometimes also used for anatomical structures. +synonym: "orthologous to" EXACT [] +xref: ECO:00000060 +xref: RO:HOM0000017 +xref: SO:0000855 +xref: SO:0000858 +xref: SO:orthologous_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000017 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_out-paralogy_relationship_with +name: in out-paralogy relationship with +def: "Paralogy that results from a duplication preceding a given speciation event." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000024] +synonym: "alloparalogy" EXACT [] +synonym: "out-paralogous to" EXACT [] +synonym: "outparalogy" EXACT [] +xref: RO:HOM0000024 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000024 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with + +[Typedef] +id: in_paedomorphorsis_relationship_with +name: in paedomorphorsis relationship with +def: "Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000029, ISBN:978-0674639416] +synonym: "juvenification" EXACT [] +synonym: "pedomorphosis" EXACT [] +xref: RO:HOM0000029 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000029 +is_symmetric: true +is_a: in_heterochronous_homology_relationship_with ! in heterochronous homology relationship with +disjoint_from: in_peramorphosis_relationship_with ! in peramorphosis relationship with + +[Typedef] +id: in_parallelism_relationship_with +name: in parallelism relationship with +def: "Homoplasy that involves homologous underlying mechanisms or structures." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000005] +comment: Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. +synonym: "parallel evolution" EXACT [] +xref: RO:HOM0000005 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000005 +is_symmetric: true +is_a: in_homoplasy_relationship_with ! in homoplasy relationship with + +[Typedef] +id: in_paralogy_relationship_with +name: in paralogy relationship with +def: "Historical homology that involves genes that diverged after a duplication event." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000011, http://www.ncbi.nlm.nih.gov/pubmed/5449325] +synonym: "paralogous to" EXACT [] +xref: RO:HOM0000011 +xref: SO:0000854 +xref: SO:0000859 +xref: SO:paralogous_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000011 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with +disjoint_from: in_orthology_relationship_with ! in orthology relationship with + +[Typedef] +id: in_paramorphism_relationship_with +name: in paramorphism relationship with +def: "Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure." [http://dx.doi.org/10.1007/s10441-007-9023-8, http://dx.doi.org/10.1046/j.1525-142x.2000.00054.x, http://purl.obolibrary.org/obo/HOM_0000074] +synonym: "axis paramorphism" RELATED [] +xref: RO:HOM0000074 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000074 +is_symmetric: true +is_a: in_homocracy_relationship_with ! in homocracy relationship with +is_a: in_iterative_homology_relationship_with ! in iterative homology relationship with + +[Typedef] +id: in_paraxenology_relationship_with +name: in paraxenology relationship with +def: "Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome." [http://purl.obolibrary.org/obo/HOM_0000068, http://www.ncbi.nlm.nih.gov/pubmed/3065587] +synonym: "duplicate xenology" EXACT [] +synonym: "multiple xenology" EXACT [] +synonym: "paraxenologous to" EXACT [] +xref: RO:HOM0000068 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000068 +is_symmetric: true +is_a: in_xenology_relationship_with ! in xenology relationship with + +[Typedef] +id: in_partial_homology_relationship_with +name: in partial homology relationship with +def: "Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous." [http://purl.obolibrary.org/obo/HOM_0000014, ISBN:0123195837, ISBN:978-0471984931] +synonym: "fractional homology" EXACT [] +synonym: "mixed homology" RELATED [] +synonym: "modular homology" RELATED [] +synonym: "partial correspondence" RELATED [] +synonym: "partial homologous to" EXACT [] +synonym: "percent homology" RELATED [] +synonym: "segmental homology" EXACT [] +xref: RO:HOM0000014 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000014 +is_symmetric: true +is_a: in_structural_homology_relationship_with ! in structural homology relationship with + +[Typedef] +id: in_peramorphosis_relationship_with +name: in peramorphosis relationship with +def: "Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits." [http://en.wikipedia.org/wiki/Peramorphosis, http://purl.obolibrary.org/obo/HOM_0000030] +xref: RO:HOM0000030 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000030 +is_symmetric: true +is_a: in_heterochronous_homology_relationship_with ! in heterochronous homology relationship with + +[Typedef] +id: in_plerology_relationship_with +name: in plerology relationship with +def: "Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution." [http://purl.obolibrary.org/obo/HOM_0000069, http://www.ncbi.nlm.nih.gov/pubmed/3065587] +comment: This phenomenon is usually due to gene conversion process. +synonym: "plerologous to" EXACT [] +xref: RO:HOM0000069 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000069 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with + +[Typedef] +id: in_plesiomorphy_relationship_with +name: in plesiomorphy relationship with +def: "Historical homology that is based on distant shared ancestry." [http://purl.obolibrary.org/obo/HOM_0000043, ISBN:978-0252068140] +comment: This term is usually contrasted to apomorphy. +synonym: "plesiomorphous to" EXACT [] +synonym: "symplesiomorphy" RELATED [] +xref: RO:HOM0000043 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000043 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_postdisplacement_relationship_with +name: in postdisplacement relationship with +def: "Paedomorphosis that is produced by delayed growth of immature structures into the adult form." [http://en.wikipedia.org/wiki/Pedomorphosis, http://purl.obolibrary.org/obo/HOM_0000051] +synonym: "post-displacement" EXACT [] +xref: RO:HOM0000051 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000051 +is_symmetric: true +is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with + +[Typedef] +id: in_pro-orthology_relationship_with +name: in pro-orthology relationship with +def: "1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000025] +synonym: "pro-orthologous to" EXACT [] +xref: RO:HOM0000025 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000025 +is_symmetric: true +is_a: in_1_to_many_orthology_relationship_with ! in 1 to many orthology relationship with + +[Typedef] +id: in_progenesis_relationship_with +name: in progenesis relationship with +def: "Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage." [http://en.wikipedia.org/wiki/Progenesis, http://purl.obolibrary.org/obo/HOM_0000031, ISBN:978-0674639416] +xref: RO:HOM0000031 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000031 +is_symmetric: true +is_a: in_paedomorphorsis_relationship_with ! in paedomorphorsis relationship with + +[Typedef] +id: in_protein_structural_homology_relationship_with +name: in protein structural homology relationship with +def: "Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence." [http://dx.doi.org/10.1016/0022-2836(76)90195-9, http://purl.obolibrary.org/obo/HOM_0000015] +synonym: "protein structural homologous to" EXACT [] +xref: MeSH:Structural_Homology\,_Protein +xref: RO:HOM0000015 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000015 +is_symmetric: true +is_a: in_structural_homology_relationship_with ! in structural homology relationship with + +[Typedef] +id: in_pseudoparalogy_relationship_with +name: in pseudoparalogy relationship with +def: "Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer." [http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000061] +comment: These genes may come out as paralogs in a single-genome analysis. +synonym: "pseudoparalogous to" EXACT [] +xref: RO:HOM0000061 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000061 +is_symmetric: true +is_a: in_xenology_relationship_with ! in xenology relationship with + +[Typedef] +id: in_regulogy_relationship_with +name: in regulogy relationship with +def: "Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms." [http://dx.doi.org/10.1101/gr.1774904, http://purl.obolibrary.org/obo/HOM_0000075] +synonym: "regulogous to" EXACT [] +xref: RO:HOM0000075 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000075 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: in_reversal_relationship_with +name: in reversal relationship with +def: "Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage." [http://dx.doi.org/10.1016/j.jhevol.2006.11.010, http://purl.obolibrary.org/obo/HOM_0000009] +synonym: "atavism" EXACT [] +synonym: "reversion" RELATED [] +synonym: "rudiment" EXACT [] +xref: RO:HOM0000009 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000009 +is_symmetric: true +is_a: in_homoplasy_relationship_with ! in homoplasy relationship with + +[Typedef] +id: in_semi-orthology_relationship_with +name: in semi-orthology relationship with +def: "1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B." [http://dx.doi.org/10.1006/scdb.1999.0338, http://dx.doi.org/10.1038/nrg2099, http://purl.obolibrary.org/obo/HOM_0000026] +comment: The converse of pro-orthologous. +synonym: "semi-orthologous to" EXACT [] +xref: RO:HOM0000026 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000026 +is_symmetric: true +is_a: in_1_to_many_orthology_relationship_with ! in 1 to many orthology relationship with + +[Typedef] +id: in_serial_homology_relationship_with +name: in serial homology relationship with +def: "Iterative homology that involves structures arranged along the main body axis." [http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000027] +synonym: "homonomy" RELATED [] +synonym: "serial homologous to" EXACT [] +xref: RO:HOM0000027 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000027 +is_symmetric: true +is_a: in_iterative_homology_relationship_with ! in iterative homology relationship with + [Typedef] id: in_similarity_relationship_with +name: in similarity relationship with +def: "Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison." [BGEE:curator, http://purl.obolibrary.org/obo/HOM_0000000] +synonym: "correspondence" RELATED [http://dx.doi.org/10.1007/BF02814479] +synonym: "resemblance" RELATED [] +synonym: "sameness" EXACT [] +synonym: "similar to" EXACT [] +xref: ECO:0000041 xref: RO:HOM0000000 +xref: SO:similar_to +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 property_value: IAO:0000116 "TODO: Add homeomorphy axiom" xsd:string property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 +property_value: seeAlso HOM:0000000 +is_symmetric: true + +[Typedef] +id: in_structural_homology_relationship_with +name: in structural homology relationship with +def: "Homology that is defined by similarity with regard to selected structural parameters." [http://dx.doi.org/10.1016/j.jhevol.2006.11.014, http://dx.doi.org/10.1146/annurev.es.20.110189.000411, http://purl.obolibrary.org/obo/HOM_0000006, ISBN:0123195837] +synonym: "idealistic homology" RELATED [] +synonym: "structural homologous to" EXACT [] +xref: ECO:0000071 +xref: MI:2163 +xref: RO:HOM0000006 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000006 +is_symmetric: true +is_a: in_homology_relationship_with ! in homology relationship with + +[Typedef] +id: in_syngeny_relationship_with +name: in syngeny relationship with +def: "Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual." [DOI:10.1002/1521-1878(200009)22\:9<846\:\:AID-BIES10>3.0.CO;2-R, http://dx.doi.org/10.1186/1742-9994-2-15, http://purl.obolibrary.org/obo/HOM_0000058] +comment: Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. +synonym: "generative homology" EXACT [] +synonym: "syngenous to" EXACT [] +xref: RO:HOM0000058 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000058 +is_symmetric: true +is_a: in_homocracy_relationship_with ! in homocracy relationship with + +[Typedef] +id: in_synology_relationship_with +name: in synology relationship with +def: "Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species." [http://dx.doi.org/10.1007/BF00173425, http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000053] +synonym: "synologous to" EXACT [] +xref: RO:HOM0000053 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000053 +is_symmetric: true +is_a: in_xenology_relationship_with ! in xenology relationship with + +[Typedef] +id: in_syntenic_homology_relationship_with +name: in syntenic homology relationship with +def: "Structural homology that is detected by similarity in content and organization between chromosomes." [http://purl.obolibrary.org/obo/HOM_0000010, MeSH:Synteny] +synonym: "syntenic homologous to" EXACT [] +synonym: "synteny" RELATED [] +xref: MeSH:Synteny +xref: RO:HOM0000010 +xref: SO:0000860 +xref: SO:0005858 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000010 +is_symmetric: true +is_a: in_structural_homology_relationship_with ! in structural homology relationship with + +[Typedef] +id: in_syntenic_orthology_relationship_with +name: in syntenic orthology relationship with +def: "Syntenic homology that involves chromosomes of different species." [http://dx.doi.org/10.1101/gr.6380007, http://purl.obolibrary.org/obo/HOM_0000013] +synonym: "syntenic orthologous to" EXACT [] +xref: RO:HOM0000013 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000013 +is_symmetric: true +is_a: in_syntenic_homology_relationship_with ! in syntenic homology relationship with + +[Typedef] +id: in_syntenic_paralogy_relationship_with +name: in syntenic paralogy relationship with +def: "Paralogy that involves sets of syntenic blocks." [DOI:10.1002/1097-010X(20001215)288\:4<345\:\:AID-JEZ7>3.0.CO;2-Y, http://dx.doi.org/10.1186/1471-213X-7-100, http://purl.obolibrary.org/obo/HOM_0000012] +synonym: "duplicon" RELATED [] +synonym: "paralogon" RELATED [] +synonym: "syntenic paralogous to" EXACT [] +xref: RO:HOM0000012 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000012 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with +is_a: in_syntenic_homology_relationship_with ! in syntenic homology relationship with + +[Typedef] +id: in_tandem_paralogy_relationship_with +name: in tandem paralogy relationship with +def: "Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://purl.obolibrary.org/obo/HOM_0000055, ISBN:978-0878932665] +synonym: "iterative paralogy" RELATED [] +synonym: "serial paralogy" RELATED [] +synonym: "tandem paralogous to" EXACT [] +xref: RO:HOM0000055 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000055 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with + +[Typedef] +id: in_taxon +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +xref: RO:0002162 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +range: CARO:0001010 +is_a: evolutionarily_related_to ! evolutionarily related to + +[Typedef] +id: in_within-species_paralogy_relationship_with +name: in within-species paralogy relationship with +def: "Paralogy that involves genes from the same species." [http://purl.obolibrary.org/obo/HOM_0000049, http://www.ensembl.org/info/docs/compara/homology_method.html] +synonym: "within-species paralogous to" EXACT [] +xref: RO:HOM0000049 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000049 +is_symmetric: true +is_a: in_paralogy_relationship_with ! in paralogy relationship with +disjoint_from: in_between-species_paralogy_relationship_with ! in between-species paralogy relationship with + +[Typedef] +id: in_xenology_relationship_with +name: in xenology relationship with +def: "Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor." [http://dx.doi.org/10.1016/S0168-9525(00)02005-9, http://dx.doi.org/10.1146/annurev.genet.39.073003.114725, http://purl.obolibrary.org/obo/HOM_0000018] +comment: The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). +synonym: "xenologous to" EXACT [] +xref: RO:HOM0000018 +property_value: http://purl.org/dc/elements/1.1/creator http://bgee.unil.ch +property_value: http://purl.org/dc/elements/1.1/source http://www.ncbi.nlm.nih.gov/pubmed/20116127 +property_value: seeAlso HOM:0000018 +is_symmetric: true +is_a: in_historical_homology_relationship_with ! in historical homology relationship with + +[Typedef] +id: only_in_taxon +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +xref: RO:0002160 +property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: in_taxon ! in taxon + +[Typedef] +id: serially_homologous_to +name: serially homologous to +xref: RO:0002159 +property_value: IAO:0000114 IAO:0000125 +is_symmetric: true +is_transitive: true +is_a: evolutionarily_related_to ! evolutionarily related to + +[Typedef] +id: shares_ancestor_with +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +xref: RO:0002158 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string +is_symmetric: true +is_transitive: true +is_a: evolutionarily_related_to ! evolutionarily related to diff --git a/subsets/ro-hom.owl b/subsets/ro-hom.owl index f7e98059..3a039acb 100644 --- a/subsets/ro-hom.owl +++ b/subsets/ro-hom.owl @@ -1,6 +1,7 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -58,15 +137,1907 @@ + + + + + + + + d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. + ancestral_stucture_of + evolutionarily_descended_from + RO:0002156 + derived_by_descent_from + derived by descent from + + + + + + + + + + + inverse of derived by descent from + RO:0002157 + + has_derived_by_descendant + has derived by descendant + + + + + + + + + + + + two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. + Consider obsoleting and merging with child relation, 'in homology relationship with' + RO:0002158 + shares_ancestor_with + VBO calls this homologous_to + shares ancestor with + + + + + + + + + + + + RO:0002159 + serially_homologous_to + serially homologous to + + + + + + + + + lactation SubClassOf 'only in taxon' some 'Mammalia' + + x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. + The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. + + 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria + + + + RO:0002160 + only_in_taxon + only in taxon + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. + + + + + RO:0002162 + + in_taxon + Connects a biological entity to its taxon of origin. + in taxon + + + + + + + + + + + RO:0002312 + evolutionary_variant_of + evolutionary variant of + + + + + + + + A relationship that holds via some environmental process + + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. + RO:0002320 + evolutionarily_related_to + evolutionarily related to + + + + + + + + + false + + x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat + + + has fused element + RO:0002374 + derived_from_ancestral_fusion_of + A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. + derived from ancestral fusion of + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. TODO: Add homeomorphy axiom + + + ECO:0000041 RO:HOM0000000 + SO:similar_to + sameness + similar to + correspondence + resemblance in_similarity_relationship_with + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + + + + + + + + + + + + Similarity that results from common evolutionary origin. + + + RO:HOM0000001 + homologous to + in_homology_relationship_with + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + + + + + + + + + + + + + Similarity that results from independent evolution. + + + RO:HOM0000002 + homoplasous to + analogy + in_homoplasy_relationship_with + in homoplasy relationship with + + + + + + Similarity that results from independent evolution. + + + + + + + + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + ECO:0000075 + RO:HOM0000003 + homocracous to + in_homocracy_relationship_with + Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. + in homocracy relationship with + + + + + + Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. + + + + + + + + + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + RO:HOM0000004 + analogy + in_convergence_relationship_with + Convergence usually implies a notion of adaptation. + in convergence relationship with + + + + + + Homoplasy that involves different underlying mechanisms or structures. + + + + + + + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + RO:HOM0000005 + parallel evolution + in_parallelism_relationship_with + Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. + in parallelism relationship with + + + + + + Homoplasy that involves homologous underlying mechanisms or structures. + + + + + + + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + ECO:0000071 + MI:2163 + RO:HOM0000006 + structural homologous to + idealistic homology + in_structural_homology_relationship_with + in structural homology relationship with + + + + + + Homology that is defined by similarity with regard to selected structural parameters. + + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by common descent. + + + homology + ECO:0000080 + RO:HOM0000007 + RO_proposed_relation:homologous_to + SO:0000330 + SO:0000853 + SO:0000857 + SO:homologous_to + TAO:homologous_to + cladistic homology + historical homologous to + phylogenetic homology + taxic homology + true homology + in_historical_homology_relationship_with + in historical homology relationship with + + + + + + Homology that is defined by common descent. + + + ISBN:0123195837 + + + + + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + ECO:0000067 + RO:HOM0000008 + biological homologous to + transformational homology + in_biological_homology_relationship_with + Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. + in biological homology relationship with + + + + + + Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. + + + + + + + + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + RO:HOM0000009 + atavism + rudiment + reversion + in_reversal_relationship_with + in reversal relationship with + + + + + + Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. + + + + + + + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + + MeSH:Synteny + RO:HOM0000010 + SO:0000860 + SO:0005858 + syntenic homologous to + synteny + in_syntenic_homology_relationship_with + in syntenic homology relationship with + + + + + + Structural homology that is detected by similarity in content and organization between chromosomes. + + MeSH:Synteny + + + + + + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + RO:HOM0000011 + SO:0000854 + SO:0000859 + SO:paralogous_to + paralogous to + in_paralogy_relationship_with + in paralogy relationship with + + + + + + Historical homology that involves genes that diverged after a duplication event. + + + + + + + + + + + + + + + Paralogy that involves sets of syntenic blocks. + + + RO:HOM0000012 + syntenic paralogous to + duplicon + paralogon + in_syntenic_paralogy_relationship_with + in syntenic paralogy relationship with + + + + + + Paralogy that involves sets of syntenic blocks. + + + DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y + + + + + + + + + + Syntenic homology that involves chromosomes of different species. + + + RO:HOM0000013 + syntenic orthologous to + in_syntenic_orthology_relationship_with + in syntenic orthology relationship with + + + + + + Syntenic homology that involves chromosomes of different species. + + + + + + + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + + RO:HOM0000014 + fractional homology + partial homologous to + segmental homology + mixed homology + modular homology + partial correspondence + percent homology + in_partial_homology_relationship_with + in partial homology relationship with + + + + + + Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. + + ISBN:0123195837 + ISBN:978-0471984931 + + + + + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + MeSH:Structural_Homology,_Protein + RO:HOM0000015 + protein structural homologous to + in_protein_structural_homology_relationship_with + in protein structural homology relationship with + + + + + + Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. + + + + + + + + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + + pseudogene + RO:HOM0000016 + SO:non_functional_homolog_of + non functional homologous to + in_non_functional_homology_relationship_with + in non functional homology relationship with + + + + + + Structural homology that involves a pseudogenic feature and its functional ancestor. + + SO:non_functional_homolog_of + + + + + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + ECO:00000060 + RO:HOM0000017 + SO:0000855 + SO:0000858 + SO:orthologous_to + orthologous to + in_orthology_relationship_with + The term is sometimes also used for anatomical structures. + in orthology relationship with + + + + + + Historical homology that involves genes that diverged after a speciation event. + + + + + + + + + + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + RO:HOM0000018 + xenologous to + in_xenology_relationship_with + The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). + in xenology relationship with + + + + + + Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. + + + + + + + + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + + RO:HOM0000019 + 1 to 1 homologous to + 1:1 homology + one-to-one homology + in_1_to_1_homology_relationship_with + in 1 to 1 homology relationship with + + + + + + Historical homology that involves two members sharing no other homologs in the lineages considered. + + BGEE:curator + + + + + + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + RO:HOM0000020 + 1 to 1 orthologous to + 1:1 orthology + one-to-one orthology + in_1_to_1_orthology_relationship_with + in 1 to 1 orthology relationship with + + + + + + Orthology that involves two genes that did not experience any duplication after the speciation event that created them. + + + + + + + + + + + + + Paralogy that results from a whole genome duplication event. + + + RO:HOM0000022 + ohnologous to + homoeology + in_ohnology_relationship_with + in ohnology relationship with + + + + + + Paralogy that results from a whole genome duplication event. + + + + + + + + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + RO:HOM0000023 + in-paralogous to + inparalogy + symparalogy + in_in-paralogy_relationship_with + in in-paralogy relationship with + + + + + + Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. + + + + + + + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + RO:HOM0000024 + alloparalogy + out-paralogous to + outparalogy + in_out-paralogy_relationship_with + in out-paralogy relationship with + + + + + + Paralogy that results from a duplication preceding a given speciation event. + + + + + + + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + RO:HOM0000025 + pro-orthologous to + in_pro-orthology_relationship_with + in pro-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. + + + + + + + + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + RO:HOM0000026 + semi-orthologous to + in_semi-orthology_relationship_with + The converse of pro-orthologous. + in semi-orthology relationship with + + + + + + 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. + + + + + + + + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + RO:HOM0000027 + serial homologous to + homonomy + in_serial_homology_relationship_with + in serial homology relationship with + + + + + + Iterative homology that involves structures arranged along the main body axis. + + + + + + + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + + RO:HOM0000028 + heterochronous homologous to + heterochrony + in_heterochronous_homology_relationship_with + in heterochronous homology relationship with + + + + + + Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. + + ISBN:978-0674639416 + + + + + + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + RO:HOM0000029 + juvenification + pedomorphosis + in_paedomorphorsis_relationship_with + in paedomorphorsis relationship with + + + + + + Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. + + + ISBN:978-0674639416 + + + + + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + RO:HOM0000030 + in_peramorphosis_relationship_with + in peramorphosis relationship with + + + + + + Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. + + + + + + + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + RO:HOM0000031 + in_progenesis_relationship_with + in progenesis relationship with + + + + + + Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. + + + ISBN:978-0674639416 + + + + + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + RO:HOM0000032 + juvenilization + neotenous to + in_neoteny_relationship_with + in neoteny relationship with + + + + + + Paedomorphosis that is produced by a retardation of somatic development. + + + ISBN:978-0674639416 + + + + + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + RO:HOM0000033 + mimicrous to + in_mimicry_relationship_with + in mimicry relationship with + + + + + + Convergence that results from co-evolution usually involving an evolutionary arms race. + + + + + + + + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + RO:HOM0000034 + 1 to many orthologous to + 1:many orthology + one-to-many orthology + co-orthology + many to 1 orthology + in_1_to_many_orthology_relationship_with + in 1 to many orthology relationship with + + + + + + Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. + + + + + + + + + + + + + Historical homology that involves two members of a larger set of homologs. + + + RO:HOM0000036 + many to many homologous to + many-to-many homology + many:many homology + in_many_to_many_homology_relationship_with + in many to many homology relationship with + + + + + + Historical homology that involves two members of a larger set of homologs. + + + + + + + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + + RO:HOM0000037 + 1 to many homologous to + one-to-many homology + 1:many homology + in_1_to_many_homology_relationship_with + in 1 to many homology relationship with + + + + + + Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. + + BGEE:curator + + + + + + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + + RO:HOM0000042 + apomorphous to + synapomorphy + in_apomorphy_relationship_with + in apomorphy relationship with + + + + + + Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. + + ISBN:978-0252068140 + + + + + + + + + + Historical homology that is based on distant shared ancestry. + + + RO:HOM0000043 + plesiomorphous to + symplesiomorphy + in_plesiomorphy_relationship_with + This term is usually contrasted to apomorphy. + in plesiomorphy relationship with + + + + + + Historical homology that is based on distant shared ancestry. + + ISBN:978-0252068140 + + + + + + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + RO:HOM0000044 + deep genetic homology + deep homologous to + generative homology + homoiology + in_deep_homology_relationship_with + Used for structures in distantly related taxa. + in deep homology relationship with + + + + + + Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. + + + + + + + + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + RO:HOM0000045 + hemiplasous to + in_hemiplasy_relationship_with + in hemiplasy relationship with + + + + + + Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. + + + + + + + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + RO:HOM0000046 + gametologous to + in_gametology_relationship_with + in gametology relationship with + + + + + + Historical homology that involves not recombining and subsequently differentiated sex chromosomes. + + + + + + + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + + MeSH:Chromosome_Pairing + RO:HOM0000047 + chromosomal homologous to + in_chromosomal_homology_relationship_with + in chromosomal homology relationship with + + + + + + Historical homology that involves the chromosomes able to pair (synapse) during meiosis. + + ISBN:0195307615 + + + + + + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + RO:HOM0000048 + many to many orthologous to + many-to-many orthology + many:many orthology + trans-orthology + co-orthology + trans-homology + in_many_to_many_orthology_relationship_with + in many to many orthology relationship with + + + + + + Orthology that involves two genes that experienced duplications more recent than the species split that created them. + + + + + + + + + + + + + + Paralogy that involves genes from the same species. + + + RO:HOM0000049 + within-species paralogous to + in_within-species_paralogy_relationship_with + in within-species paralogy relationship with + + + + + + Paralogy that involves genes from the same species. + + + + + + + + + + + + Paralogy that involves genes from different species. + + + RO:HOM0000050 + between-species paralogous to + in_between-species_paralogy_relationship_with + The genes have diverged before a speciation event. + in between-species paralogy relationship with + + + + + + Paralogy that involves genes from different species. + + + + + + + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + RO:HOM0000051 + post-displacement + in_postdisplacement_relationship_with + in postdisplacement relationship with + + + + + + Paedomorphosis that is produced by delayed growth of immature structures into the adult form. + + + + + + + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + RO:HOM0000052 + in_hypermorphosis_relationship_with + in hypermorphosis relationship with + + + + + + Peramorphosis that is produced by a delay in the offset of development. + + + ISBN:978-0674639416 + + + + + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + RO:HOM0000053 + synologous to + in_synology_relationship_with + in synology relationship with + + + + + + Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. + + + + + + + + + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + ECO:0000080 + RO:HOM0000054 + isoorthologous to + in_isoorthology_relationship_with + in isoorthology relationship with + + + + + + Orthology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + RO:HOM0000055 + tandem paralogous to + iterative paralogy + serial paralogy + in_tandem_paralogy_relationship_with + in tandem paralogy relationship with + + + + + + Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. + + + ISBN:978-0878932665 + + + + + + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + RO:HOM0000057 + apomorphic tendency + cryptic homology + latent homologous to + underlying synapomorphy + homoiology + homoplastic tendency + re-awakening + in_latent_homology_relationship_with + Used for structures in closely related taxa. + in latent homology relationship with + + + + + + Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). + + + + + ISBN:0199141118 + + + + + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + RO:HOM0000058 + generative homology + syngenous to + in_syngeny_relationship_with + Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. + in syngeny relationship with + + + + + + Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. + + + DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R + + + + + + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + RO:HOM0000060 + 1:1 paralogy + apparent 1:1 orthology + apparent orthologous to + pseudoorthology + in_apparent_orthology_relationship_with + The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. + in apparent orthology relationship with + + + + + + Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. + + + + + + + + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + RO:HOM0000061 + pseudoparalogous to + in_pseudoparalogy_relationship_with + These genes may come out as paralogs in a single-genome analysis. + in pseudoparalogy relationship with + + + + + + Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. + + + + + + + + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + RO:HOM0000062 + equivalogous to + in_equivalogy_relationship_with + This may include examples of orthology, paralogy and xenology. + in equivalogy relationship with + + + + + + Historical homology that involves functional equivalent genes with retention of the ancestral function. + + + + + + + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + RO:HOM0000063 + interologous to + in_interology_relationship_with + in interology relationship with + + + + + + Historical homology that involves orthologous pairs of interacting molecules in different organisms. + + + + + + + + + + + + + Similarity that is characterized by interchangeability in function. + + + RO:HOM0000065 + functional similarity + in_functional_equivalence_relationship_with + in functional equivalence relationship with + + + + + Similarity that is characterized by interchangeability in function. + + + + + + + + + + + + + Biological homology that involves parts of the same organism. + + + RO:HOM0000066 + iterative homologous to + in_iterative_homology_relationship_with + in iterative homology relationship with + + + + + + Biological homology that involves parts of the same organism. + + + + + + + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + RO:HOM0000068 + duplicate xenology + multiple xenology + paraxenologous to + in_paraxenology_relationship_with + in paraxenology relationship with + + + + + + Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. + + + + + + + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + RO:HOM0000069 + plerologous to + in_plerology_relationship_with + This phenomenon is usually due to gene conversion process. + in plerology relationship with + + + + + + Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. + + + + + + + + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + RO:HOM0000071 + homotopous to + in_homotopy_relationship_with + Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. + in homotopy relationship with + + + + + + Structural homology that involves structures with the same or similar relative positions. + + + + ISBN:0123195837 + + + + + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + RO:HOM0000072 + heterotopy + in_homeosis_relationship_with + in homeosis relationship with + + + + + + Biological homology that involves an ectopic structure and the normally positioned structure. + + + + + + + + + + + + + + Synology that results from allopolyploidy. + + + RO:HOM0000073 + homoeologous to + in_homoeology_relationship_with + On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. + in homoeology relationship with + + + + + + Synology that results from allopolyploidy. + + + + + + + + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + RO:HOM0000074 + axis paramorphism + in_paramorphism_relationship_with + in paramorphism relationship with + + + + + + Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. + + + + + + + + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + RO:HOM0000075 + regulogous to + in_regulogy_relationship_with + in regulogy relationship with + + + + + + Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. + + + + + + + + + + + + + + diff --git a/subsets/ro-hom.tsv b/subsets/ro-hom.tsv new file mode 100644 index 00000000..9e64d1bd --- /dev/null +++ b/subsets/ro-hom.tsv @@ -0,0 +1,2 @@ +?x ?label + diff --git a/subsets/ro-interaction.json b/subsets/ro-interaction.json new file mode 100644 index 00000000..67569205 --- /dev/null +++ b/subsets/ro-interaction.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-interaction.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_2D_boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_2D_boundary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002003", + "lbl" : "electrically_synapsed_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two neurons that are electrically coupled via gap junctions." + }, + "xrefs" : [ { + "val" : "RO:0002003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "electrically_synapsed_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002007" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002008", + "lbl" : "coincident with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." + }, + "comments" : [ "Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002008" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Note from NCEAS meeting: consider changing primary label" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "coincident_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002010", + "lbl" : "regulates in other organism", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2)." + }, + "xrefs" : [ { + "val" : "RO:0002010" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_in_other_organism" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002012", + "lbl" : "occurrent part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A part of relation that applies only between occurrents." + }, + "xrefs" : [ { + "val" : "RO:0002012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurrent_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002013", + "lbl" : "has regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." + }, + "xrefs" : [ { + "val" : "RO:0002013" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:30:46Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002014", + "lbl" : "has negative regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'." ], + "xrefs" : [ { + "val" : "RO:0002014" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:01Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_negative_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002015", + "lbl" : "has positive regulatory component activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." + }, + "comments" : [ "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'." ], + "xrefs" : [ { + "val" : "RO:0002015" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:31:17Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_positive_regulatory_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002016", + "lbl" : "has necessary component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity." ], + "xrefs" : [ { + "val" : "RO:0002016" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:36:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_necessary_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002017", + "lbl" : "has component activity", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], + "xrefs" : [ { + "val" : "RO:0002017" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:44:33Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002018", + "lbl" : "has component process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "xrefs" : [ { + "val" : "RO:0002018" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-05-24T09:49:21Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002019", + "lbl" : "has ligand", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." + }, + "xrefs" : [ { + "val" : "RO:0002019" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-19T17:30:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ligand" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002020", + "lbl" : "transports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another." + }, + "xrefs" : [ { + "val" : "RO:0002020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:11:08Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." + }, + "xrefs" : [ { + "val" : "RO:0002021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002022", + "lbl" : "directly regulated by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ], + "xrefs" : [ { + "val" : "RO:0002022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:24Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002023", + "lbl" : "directly negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:38Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002024", + "lbl" : "directly positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. 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No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." + }, + "xrefs" : [ { + "val" : "RO:0002104" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9990-8331" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : 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"synapsed_via_type_Is_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type Is bouton." + }, + "comments" : [ "Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002106" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-5948-3092" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that 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it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002113" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "synapses in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_presynaptic_terminal_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002114", + "lbl" : "synapsed_via_type_III_bouton_to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a motor neuron and a muscle that it synapses to via a type III bouton." + }, + "comments" : [ "Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y))))" ], + "xrefs" : [ { + "val" : "RO:0002114" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_via_type_III_bouton_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002115", + "lbl" 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 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}, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002297" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002298" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_morphogenesis_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_maturation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002300", + "lbl" : "results in disappearance of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002300" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "foramen ovale closure SubClassOf results in disappearance of foramen ovale" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_disappearance_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002301", + "lbl" : "results in developmental regression of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002301" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "May be merged into parent relation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_regression_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002302", + "lbl" : "is treated by substance", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of 'is substance that treats'" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002302" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_treated_by_substance" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002303", + "lbl" : "has habitat", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs." + }, + "comments" : [ "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002303" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-4366-3088" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for living in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_habitat" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + }, + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002304" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_positive_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002305", + "lbl" : "causally upstream of, negative effect", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002305" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://purl.org/dc/terms/creator", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_negative_effect" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002309", + "lbl" : "has exposure stimulus", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002309" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6996-0040" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-8461-9745" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-06-05T17:35:04Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stimulus" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002313", + "lbl" : "transports or maintains localization of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002313" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "regulates localization of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transports_or_maintains_localization_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." + }, + "xrefs" : [ { + "val" : "RO:0002314" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres in part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : 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"http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GOC:mtg_berkeley_2013" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_acquisition_of_features_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002321", + "lbl" : "ecologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002321" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "colocalizes_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002326", + "lbl" : "contributes to", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002326" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002327", + "lbl" : "enables", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c enables p iff c is capable of p and c acts to execute p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002327" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "catalyzes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is catalyzing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is executing" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enables" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + }, + "xrefs" : [ { + "val" : "RO:0002328" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "functionally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + }, + "xrefs" : [ { + "val" : "RO:0002329" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_structure_that_is_capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002331", + "lbl" : "involved in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" + }, + "xrefs" : [ { + "val" : "RO:0002331" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "actively involved in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "enables part of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Involved_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" + }, + "xrefs" : [ { + "val" : "RO:0002332" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates levels of (process to entity)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_levels_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002333", + "lbl" : "enabled by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of enables" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002333" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "enabled_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002334" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulated by (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of negatively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002335" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002336" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002337", + "lbl" : "related via localization to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds via some process of localization" + }, + "xrefs" : [ { + "val" : "RO:0002337" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is a grouping relation." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_localization_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002338", + "lbl" : "has target start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002338" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002339" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002340", + "lbl" : "imports", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002340" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "imports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " + }, + "xrefs" : [ { + "val" : "RO:0002341" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_along" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], + "xrefs" : [ { + "val" : "RO:0002342" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_across" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002343" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_growth_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002344" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'mitochondrial transport' 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"http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "exports" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002348", + "lbl" : "results in commitment to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002348" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron." + }, { 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. 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It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. 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"RO:0002445" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has parasite" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "parasitised by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitized_by" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://eol.org/schema/terms/hasParasite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002446", + "lbl" : "participates in a abiotic-biotic interaction with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. 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We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "subject_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002463", + "lbl" : "target participant in", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002463" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "target_participant_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002469", + "lbl" : "provides nutrients for", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002469" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_nutrients_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002470", + "lbl" : "eats", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002470" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is subject of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "eats" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002471", + "lbl" : "is eaten by", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002471" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "eaten by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is target of eating interaction with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_eaten_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002473" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "composed_primarily_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002476", + "lbl" : "child nucleus of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d" + }, + "xrefs" : [ { + "val" : "RO:0002476" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "ABal nucleus child nucleus of ABa nucleus (in C elegans)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/subsets/ro-interaction.obo b/subsets/ro-interaction.obo index 521beb78..57efd25a 100644 --- a/subsets/ro-interaction.obo +++ b/subsets/ro-interaction.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-interaction -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/subsets/ro-interaction.owl b/subsets/ro-interaction.owl index 1f7b268f..4a151349 100644 --- a/subsets/ro-interaction.owl +++ b/subsets/ro-interaction.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-interaction.tsv b/subsets/ro-interaction.tsv new file mode 100644 index 00000000..352e8a3b --- /dev/null +++ b/subsets/ro-interaction.tsv @@ -0,0 +1,51 @@ +?x ?label +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid1 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid18 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid22 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid26 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid33 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid37 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid40 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid5 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid52 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid58 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid61 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid64 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid67 +_:B1440b171X2Dff4aX2D4333X2D9a75X2Da213cd8e0fb1genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-mereotopology.json b/subsets/ro-mereotopology.json new file mode 100644 index 00000000..2e50b0cc --- /dev/null +++ b/subsets/ro-mereotopology.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-mereotopology.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : 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For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "xrefs" : [ { + "val" : "RO:0002085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "di" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "encompasses" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_after" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "xrefs" : [ { + "val" : "RO:0002087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "lbl" : "during which starts", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002215" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "xrefs" : [ { + "val" : "RO:0002216" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "xrefs" : [ { + "val" : "RO:0002219" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002220" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "adjacent_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002221" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounds" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "temporally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002223" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Allen" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002224" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "xrefs" : [ { + "val" : "RO:0002225" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "xrefs" : [ { + "val" : "RO:0002226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + }, + "xrefs" : [ { + "val" : "RO:0002227" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "obligate_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + }, + "xrefs" : [ { + "val" : "RO:0002228" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "facultative_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ends with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002229" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002230" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "finished by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002231" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002232" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002233" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002234" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_output" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + }, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ 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the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : 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It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. 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Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). 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Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "xrefs" : [ { + "val" : "RO:0002372" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_origin" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "xrefs" : [ { + "val" : "RO:0002373" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_insertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "xrefs" : [ { + "val" : "RO:0002375" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "interacts_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002435" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/subsets/ro-mereotopology.obo b/subsets/ro-mereotopology.obo index 33d6e97a..ba745b5e 100644 --- a/subsets/ro-mereotopology.obo +++ b/subsets/ro-mereotopology.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-mereotopology -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/subsets/ro-mereotopology.owl b/subsets/ro-mereotopology.owl index 55296922..6b552729 100644 --- a/subsets/ro-mereotopology.owl +++ b/subsets/ro-mereotopology.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-mereotopology.tsv b/subsets/ro-mereotopology.tsv new file mode 100644 index 00000000..68694895 --- /dev/null +++ b/subsets/ro-mereotopology.tsv @@ -0,0 +1,51 @@ +?x ?label +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid1 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid18 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid22 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid26 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid33 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid37 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid40 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid5 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid52 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid58 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid61 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid64 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid67 +_:B55a3cba6X2Dfec8X2D4bf0X2D90feX2D3339107f0ea9genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-sequence.json b/subsets/ro-sequence.json new file mode 100644 index 00000000..3d3191dc --- /dev/null +++ b/subsets/ro-sequence.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-sequence.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : 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For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "xrefs" : [ { + "val" : "RO:0002085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "di" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "encompasses" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_after" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "xrefs" : [ { + "val" : "RO:0002087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "lbl" : "during which starts", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002215" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "xrefs" : [ { + "val" : "RO:0002216" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "xrefs" : [ { + "val" : "RO:0002219" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002220" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "adjacent_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002221" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounds" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "temporally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002223" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Allen" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002224" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "xrefs" : [ { + "val" : "RO:0002225" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "xrefs" : [ { + "val" : "RO:0002226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + }, + "xrefs" : [ { + "val" : "RO:0002227" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "obligate_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + }, + "xrefs" : [ { + "val" : "RO:0002228" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "facultative_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ends with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002229" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002230" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "finished by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002231" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002232" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002233" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002234" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_output" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + }, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ 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the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : 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It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. 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Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). 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Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "xrefs" : [ { + "val" : "RO:0002372" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_origin" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "xrefs" : [ { + "val" : "RO:0002373" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_insertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "xrefs" : [ { + "val" : "RO:0002375" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "interacts_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002435" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/subsets/ro-sequence.obo b/subsets/ro-sequence.obo index 3df12e6c..fde68107 100644 --- a/subsets/ro-sequence.obo +++ b/subsets/ro-sequence.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-sequence -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/subsets/ro-sequence.owl b/subsets/ro-sequence.owl index bfa36ffb..4482b19b 100644 --- a/subsets/ro-sequence.owl +++ b/subsets/ro-sequence.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-sequence.tsv b/subsets/ro-sequence.tsv new file mode 100644 index 00000000..8f592795 --- /dev/null +++ b/subsets/ro-sequence.tsv @@ -0,0 +1,51 @@ +?x ?label +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid1 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid18 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid22 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid26 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid33 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid37 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid40 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid5 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid52 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid58 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid61 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid64 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid67 +_:B21d9ed84X2Dc88eX2D4b40X2Db405X2Dbe4df60e6e65genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-time-interval.json b/subsets/ro-time-interval.json new file mode 100644 index 00000000..47bf0880 --- /dev/null +++ b/subsets/ro-time-interval.json @@ -0,0 +1,14062 @@ +{ + "graphs" : [ { + "id" : "http://purl.obolibrary.org/obo/ro/subsets/ro-time-interval.owl", + "nodes" : [ { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "is part of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my brain is part of my body (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this day is part of this year (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "part_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000002" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000003" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000004" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000017" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000019" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000020" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0040042", + "val" : "http://purl.obolibrary.org/obo/BFO_0000031" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has part", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has part" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has part my brain (continuant parthood, two material entities)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this year has part this day (occurrent parthood)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_part" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is preceded by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "preceded_by" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "precedes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ], + "xrefs" : [ { + "val" : "RO:0000052" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "inheres in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this fragility is a characteristic of this vase" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a characteristic of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "inheres_in" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "characteristic_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple is bearer of this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this vase is bearer of this fragility" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "bearer_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is bearer of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_characteristic" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "participates in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood clot participates in this blood coagulation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this input material (or this output material) participates in this process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator participates in this investigation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "participates_in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", + "val" : "has participant" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this blood coagulation has participant this blood clot" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigation has participant this investigator" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this process has participant this input material (or this output material)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_participant" + }, { + "pred" : "http://purl.org/dc/elements/1.1/source", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000079", + "lbl" : "function of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000079" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this catalysis function is a function of this enzyme" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "function_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is function of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "function_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000080" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this red color is a quality of this apple" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is quality of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "quality_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "quality_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000081", + "lbl" : "role of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "xrefs" : [ { + "val" : "RO:0000081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this investigator role is a role of this person" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is role of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "role_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "role_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000085", + "lbl" : "has function", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_function" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_function" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this apple has quality this red color" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_quality" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000087", + "lbl" : "has role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has_role" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000091", + "lbl" : "has disposition", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" + }, + "xrefs" : [ { + "val" : "RO:0000091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_disposition" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000092", + "lbl" : "disposition of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has disposition" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0000092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "disposition_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001020", + "lbl" : "is allergic trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001020" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_allergic_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001021", + "lbl" : "is autoimmune trigger for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_autoimmune_trigger_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001022", + "lbl" : "has allergic trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001022" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_allergic_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001023", + "lbl" : "has autoimmune trigger", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity." + }, + "xrefs" : [ { + "val" : "RO:0001023" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_autoimmune_trigger" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "the surface of my skin is a 2D boundary of my body" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "2D_boundary_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is 2D boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "is boundary of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "surface of" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "2D_boundary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "xrefs" : [ { + "val" : "RO:0002002" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "my body has 2D boundary the surface of my skin" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has boundary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : 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For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002024" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-17T13:52:47Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_positively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002025", + "lbl" : "has effector activity", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.", + "xrefs" : [ "GOC:dos" ] + }, + "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], + "xrefs" : [ { + "val" : "RO:0002025" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-09-22T14:14:36Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_effector_activity" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002026", + "lbl" : "in register with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two images, A and B, where:\nA depicts X;\nB depicts Y;\nX and Y are both of type T'\nC is a 2 layer image consiting of layers A and B;\nA and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other.\nNote: A and B may be 2D or 3D.\nExamples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software.", + "xrefs" : [ "GOC:dos" ] + }, + "xrefs" : [ { + "val" : "RO:0002026" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "dos" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-12-07T12:58:06Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_register_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002081" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "<=" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before_or_simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002082" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "simultaneous_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002083", + "lbl" : "before", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002083" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002084", + "lbl" : "during which ends", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002084" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002085", + "lbl" : "encompasses", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "xrefs" : [ { + "val" : "RO:0002085" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "di" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "encompasses" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002086" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_after" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "xrefs" : [ { + "val" : "RO:0002087" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts_at_end_of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002088", + "lbl" : "during which starts", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002088" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "during_which_starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002089", + "lbl" : "starts before", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002089" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_before" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002090" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends_at_start_of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "meets" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/BFO_0000063" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002091", + "lbl" : "starts during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002091" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "io" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002092", + "lbl" : "happens during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002092" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "d" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "during" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "happens_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002093", + "lbl" : "ends during", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). " ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002093" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "David Osumi-Sutherland" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "o" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "overlaps" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_during" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and an anatomical structure that its soma is part of." + }, + "xrefs" : [ { + "val" : "RO:0002100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_soma_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + }, + "xrefs" : [ { + "val" : "RO:0002101" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "fasciculates with" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(fasciculates_with ?x ?y)\n\t\t(exists (?nps ?npbs)\n\t\t\t(and \n\t\t\t\t(\"neuron ; CL_0000540\" ?x)\n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?y) \n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n\t\t\t\t(part_of ?npbs ?y) \t\t\t\n\t\t\t\t(part_of ?nps ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "fasciculates_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." + }, + "xrefs" : [ { + "val" : "RO:0002102" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "axon_synapses_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " + }, + "xrefs" : [ { + "val" : "RO:0002103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "synapsed_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma 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between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + }, + "xrefs" : [ { + "val" : "RO:0002130" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has synapse in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_synaptic_terminal_in" + } ] + } + 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"overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + }, + "xrefs" : [ { + "val" : "RO:0002132" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has fasciculating component" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_fasciculating_neuron_projection" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "xrefs" : [ { + "val" : "RO:0002150" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "connected to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "continuous_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002151", + "lbl" : "partially overlaps", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002151" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "proper overlaps" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", + "val" : "(forall (?x ?y) \n\t(iff \n\t\t(proper_overlaps ?x ?y)\n\t\t(and \n\t\t\t(overlaps ?x ?y)\n\t\t\t(not (part_of ?x ?y)) \n\t\t\t(not (part_of ?y ?x)))))" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "partially_overlaps" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002163" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "spatially_disjoint_from" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, + "xrefs" : [ { + "val" : "RO:0002170" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connected_to" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + }, + "xrefs" : [ { + "val" : "RO:0002176" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The M8 connects Glasgow and Edinburgh" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connects" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + }, + "xrefs" : [ { + "val" : "RO:0002177" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to part of (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, + "xrefs" : [ { + "val" : "RO:0002178" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "supplies" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + }, + "xrefs" : [ { + "val" : "RO:0002179" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "drains" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002180" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002200", + "lbl" : "has phenotype", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype)." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_phenotype" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002201", + "lbl" : "phenotype of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has phenotype" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002201" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "phenotype_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ], + "xrefs" : [ { + "val" : "RO:0002202" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002203" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" + } ], + "xrefs" : [ { + "val" : "RO:0002207" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "FBbt" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002202" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002208", + "lbl" : "parasitoid of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite that kills or sterilizes its host" + }, + "xrefs" : [ { + "val" : "RO:0002208" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "parasitoid_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002209", + "lbl" : "has parasitoid", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of parasitoid of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002209" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_parasitoid" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002210" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "developmental precursor of" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_develops_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-7476-6306" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-3837-8864" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "regulates (processual)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", + "val" : "false" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "negatively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "positively regulates (process to process)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002215" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function realized in" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + }, + "xrefs" : [ { + "val" : "RO:0002216" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "has function in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + }, + "xrefs" : [ { + "val" : "RO:0002219" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002220" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "adjacent_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of surrounded by" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002221" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "surrounds" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002222" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "temporally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002223" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Allen" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002224" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + }, + "xrefs" : [ { + "val" : "RO:0002225" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_from_part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + }, + "xrefs" : [ { + "val" : "RO:0002226" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "EHDAA2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Jonathan Bard, EHDAA2" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "develops_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002227", + "lbl" : "obligate parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host." + }, + "xrefs" : [ { + "val" : "RO:0002227" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "obligate_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002228", + "lbl" : "facultative parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host." + }, + "xrefs" : [ { + "val" : "RO:0002228" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "facultative_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of ends with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002229" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002230" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "Chris Mungall" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "finished by" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002231" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "starts with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002232" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "ends with process that occurs in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_end_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002233" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "consumes" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002234" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "produces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_output" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002235", + "lbl" : "stem parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047)" + }, + "xrefs" : [ { + "val" : "RO:0002235" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "stem_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002236", + "lbl" : "root parasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005)" + }, + "xrefs" : [ { + "val" : "RO:0002236" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "root_parasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002237", + "lbl" : "hemiparasite of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well." + }, + "xrefs" : [ { + "val" : "RO:0002237" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "hemiparasite_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002238", + "lbl" : "has component participant", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys." + }, + "xrefs" : [ { + "val" : "RO:0002238" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9625-1899" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002240", + "lbl" : "has exposure receptor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000001" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_receptor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002241", + "lbl" : "has exposure stressor", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." + }, + "xrefs" : [ { + "val" : "RO:0002241" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000000" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_stressor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002242", + "lbl" : "has exposure route", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" + }, + "xrefs" : [ { + "val" : "RO:0002242" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "ExO:0000055" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_route" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002243", + "lbl" : "has exposure transport path", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A broad relationship between an exposure event or process and the course takes from the source to the target." + }, + "xrefs" : [ { + "val" : "RO:0002243" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ExO_0000004" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_exposure_transport_path" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002244", + "lbl" : "related via exposure to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Any relationship between an exposure event or process and any other entity." + }, + "xrefs" : [ { + "val" : "RO:0002244" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "related_via_exposure_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002248", + "lbl" : "has active ingredient", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "has active substance" + }, { + "pred" : "hasRelatedSynonym", + "val" : "has active pharmaceutical ingredient" + } ], + "xrefs" : [ { + "val" : "RO:0002248" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Any portion of roundup 'has active ingredient' some glyphosate" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_active_ingredient" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002249", + "lbl" : "active ingredient in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has active ingredient" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "active_ingredient_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." + }, + "xrefs" : [ { + "val" : "RO:0002252" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "connecting_branch_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of connecting branch of" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002253" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_connecting_branch" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002254", + "lbl" : "has developmental contribution from", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" + }, + "xrefs" : [ { + "val" : "RO:0002254" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_contribution_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002255", + "lbl" : "developmentally contributes to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has developmental contribution from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002255" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_contributes_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002256", + "lbl" : "developmentally induced by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" + }, + "xrefs" : [ { + "val" : "RO:0002256" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "induced by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "GO:0001759" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induced_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002257", + "lbl" : "developmentally induces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally induced by" + }, + "xrefs" : [ { + "val" : "RO:0002257" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_induces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002258", + "lbl" : "developmentally preceded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" + }, + "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], + "xrefs" : [ { + "val" : "RO:0002258" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002260", + "lbl" : "has biological role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" + }, + "xrefs" : [ { + "val" : "RO:0002260" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_biological_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002261", + "lbl" : "has application role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" + }, + "xrefs" : [ { + "val" : "RO:0002261" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_application_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002262", + "lbl" : "has chemical role", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" + }, + "xrefs" : [ { + "val" : "RO:0002262" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_chemical_role" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002263" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002264" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "acts_upstream_of_or_within" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" + }, + "xrefs" : [ { + "val" : "RO:0002285" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "replaces" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_replaces" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "Inverse of developmentally preceded by" + }, + "xrefs" : [ { + "val" : "RO:0002286" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_succeeded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002287" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of_developmental_precursor_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." + }, + "xrefs" : [ { + "val" : "RO:0002295" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002296" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.geneontology.org/GO.doc.development.shtml" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ 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the entity over time that is independent of changes in it's shape and results in an end point state of that entity." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002299" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000125" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : 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It is intended as a grouping for a diverse set of relations, all involving ecological interactions" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ecologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002322", + "lbl" : "confers advantage in", + "type" : "PROPERTY", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002322" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. 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Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "adapted for" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "confers_advantage_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + }, + "xrefs" : [ { + "val" : "RO:0002323" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0001900", + "val" : "http://purl.obolibrary.org/obo/RO_0001901" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "mereotopologically_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + }, + "xrefs" : [ { + "val" : "RO:0002324" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "developmentally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002325", + "lbl" : "colocalizes with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "xrefs" : [ { + "val" : "RO:0002325" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). 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Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. 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" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002356" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_specification_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002357", + "lbl" : "results in developmental induction of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c." + }, + "xrefs" : [ { + "val" : "RO:0002357" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_induction_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.org/dc/terms/source", + "val" : "http://neurolex.org/wiki/Property:DendriteLocation" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_dendrite_location" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002371" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "attached to (anatomical structure to anatomical structure)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "attached_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "xrefs" : [ { + "val" : "RO:0002372" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_origin" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/origin" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." + }, + "xrefs" : [ { + "val" : "RO:0002373" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "Wikipedia:Insertion_(anatomy)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_muscle_insertion" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "xrefs" : [ { + "val" : "RO:0002375" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004036", + "val" : "http://purl.obolibrary.org/obo/BFO_0000050" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "in_branching_relationship_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. 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If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River tributary_of Columbia River" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "inferior epigastric vein tributary_of external iliac vein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains into" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "drains to" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "tributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Tributary" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.medindia.net/glossary/venous_tributary.htm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "tributary_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002377", + "lbl" : "distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x" + }, + "comments" : [ "This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Deschutes River distributary_of Little Lava Lake" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "branch of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "distributary channel of" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://en.wikipedia.org/wiki/Distributary" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002378", + "lbl" : "anabranch of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002378" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "anastomoses with" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "anabranch_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + }, + "xrefs" : [ { + "val" : "RO:0002379" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A lump of clay and a statue" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This relation is added for formal completeness. 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B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "branching_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002381", + "lbl" : "main stem of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002381" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "main_stem_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002382", + "lbl" : "proper distributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_distributary_of y iff x distributary_of y and x does not flow back into y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002382" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_distributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002383", + "lbl" : "proper tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x proper_tributary_of y iff x tributary_of y and x does not originate from y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002383" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "proper_tributary_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + }, + "xrefs" : [ { + "val" : "RO:0002384" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_developmental_potential_involving" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + }, + "xrefs" : [ { + "val" : "RO:0002385" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_contribute_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + }, + "xrefs" : [ { + "val" : "RO:0002386" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_developmentally_induce" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002387" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + }, + "xrefs" : [ { + "val" : "RO:0002388" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_potential_to_directly_develop_into" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002400", + "lbl" : "has direct input", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p." + }, + "xrefs" : [ { + "val" : "RO:0002400" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "'protein catabolic process' SubClassOf has_direct_input some protein" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly consumes" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_direct_input" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" + }, + "xrefs" : [ { + "val" : "RO:0002404" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002405", + "lbl" : "immediately causally downstream of", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002405" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_downstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002407", + "lbl" : "indirectly positively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002407" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly activates" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002213" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_positively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002409", + "lbl" : "indirectly negatively regulates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." + }, + "xrefs" : [ { + "val" : "RO:0002409" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "indirectly inhibits" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002579", + "val" : "http://purl.obolibrary.org/obo/RO_0002212" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "indirectly_negatively_regulates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] + }, + "xrefs" : [ { + "val" : "RO:0002410" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002411" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002412", + "lbl" : "immediately causally upstream of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." + }, + "xrefs" : [ { + "val" : "RO:0002412" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_causally_upstream_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002413", + "lbl" : "provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c." + }, + "xrefs" : [ { + "val" : "RO:0002413" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "directly provides input for" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "directly provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002414", + "lbl" : "transitively provides input for", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "transitive form of directly_provides_input_for" + }, + "xrefs" : [ { + "val" : "RO:0002414" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", + "val" : "http://purl.obolibrary.org/obo/IAO_0000428" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", + "val" : "transitively provides input for (process to process)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transitively_provides_input_for" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." + }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "affects" + } ], + "xrefs" : [ { + "val" : "RO:0002418" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "influences (processual)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of causally upstream of or within" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002427" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002428" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002429", + "lbl" : "involved in positive regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002429" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004049", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_positive_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002430", + "lbl" : "involved in negative regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" + }, + "xrefs" : [ { + "val" : "RO:0002430" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002428" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_negative_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" + }, + "xrefs" : [ { + "val" : "RO:0002431" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "involved in or reguates" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "involved_in_or_involved_in_regulation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002432", + "lbl" : "is active in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", + "xrefs" : [ "GOC:cjm", "GOC:dos" ] + }, + "comments" : [ "" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "enables activity in" + } ], + "xrefs" : [ { + "val" : "RO:0002432" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "A protein that enables activity in a cytosol." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "executes activity in" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "is_active_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + }, + "xrefs" : [ { + "val" : "RO:0002433" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "contributes_to_morphology_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002434", + "lbl" : "interacts with", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "in pairwise interaction with" + } ], + "xrefs" : [ { + "val" : "RO:0002434" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Considering relabeling as 'pairwise interacts with'" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "interacts_with" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" + }, { + "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", + "val" : "http://purl.obolibrary.org/obo/MI_0914" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002435", + "lbl" : "genetically interacts with", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002435" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : 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For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "molecularly controls" + } ], + "xrefs" : [ { + "val" : "RO:0002448" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0003-4639-4431" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "directly_regulates_activity_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002449", + "lbl" : "directly negatively regulates activity of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase 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However, it is applicable to any organismal cell lineage." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002477", + "lbl" : "child nucleus of in hermaphrodite", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a hermaphroditic organism" + }, + "xrefs" : [ { + "val" : "RO:0002477" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_hermaphrodite" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002478", + "lbl" : "child nucleus of in male", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A child nucleus relationship in which the cells are part of a male organism" + }, + "xrefs" : [ { + "val" : "RO:0002478" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "child_nucleus_of_in_male" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002479" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part_that_occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002480", + "lbl" : "ubiquitinates", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y" + }, + "xrefs" : [ { + "val" : "RO:0002480" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Axiomatization to GO to be added later" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ubiquitinates" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002485" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "receives_input_from" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "meta" : { + "xrefs" : [ { + "val" : "RO:0002486" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sends_output_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + }, + "xrefs" : [ { + "val" : "RO:0002494" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + }, + "xrefs" : [ { + "val" : "RO:0002495" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002575", + "val" : "http://purl.obolibrary.org/obo/RO_0002494" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediate_transformation_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + }, + "xrefs" : [ { + "val" : "RO:0002500" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causal_agent_in_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + }, + "xrefs" : [ { + "val" : "RO:0002501" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. 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" + }, + "xrefs" : [ { + "val" : "RO:0002514" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", + "val" : "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "sequentially_related_to" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002515", + "lbl" : "sequentially adjacent to", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y" + }, + "xrefs" : [ { + "val" : "RO:0002515" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every UTR is adjacent to a CDS of the same transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Two consecutive DNA residues are 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"basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", + "val" : "Every CDS has as a start sequence the start codon for that transcript" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", + "val" : "started by" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", + "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20226267" + }, { + "pred" : "http://purl.org/spar/cito/citesAsAuthority", + "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_sequence" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002517", + "lbl" : "is start sequence of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "inverse of has start sequence" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], 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"http://purl.obolibrary.org/obo/BFO_0000017" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004020", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000006" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004021", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/RO_0004030", + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/CARO_0000003" ] + } ] + } ] +} \ No newline at end of file diff --git a/subsets/ro-time-interval.obo b/subsets/ro-time-interval.obo index 7aeb28f2..8150a607 100644 --- a/subsets/ro-time-interval.obo +++ b/subsets/ro-time-interval.obo @@ -1,12 +1,22 @@ format-version: 1.2 ontology: ro/subsets/ro-time-interval -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (coincident with)\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (synapsed by)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (has fasciculating neuron projection)\n\nObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: (connected to)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (connects)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (directly develops from)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (anabranch of)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n# Object Property: (branching part of)\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: (has skeleton)\n\nIrreflexiveObjectProperty()\n\n# Object Property: (condition has genetic basis in)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has basis in feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has location)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has inflammation site)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: (disease has feature)\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n\n\n\nAnnotationAssertion(rdfs:comment \"\")\n) [Typedef] id: 2D_boundary_of +name: 2D boundary of +def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] xref: RO:0002000 +property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +property_value: IAO:0000118 "2D_boundary_of" xsd:string +property_value: IAO:0000118 "boundary of" xsd:string +property_value: IAO:0000118 "is 2D boundary of" xsd:string +property_value: IAO:0000118 "is boundary of" xsd:string property_value: IAO:0000118 "surface of" xsd:string +property_value: RO:0001900 RO:0001901 is_a: mereotopologically_related_to ! mereotopologically related to +inverse_of: has_2D_boundary ! has 2D boundary [Typedef] id: acquires_nutrients_from @@ -24,7 +34,7 @@ name: active ingredient in def: "inverse of has active ingredient" [] subset: RO:0002259 xref: RO:0002249 -is_a: part_of +is_a: part_of ! part of [Typedef] id: acts_on_population_of @@ -34,7 +44,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0012003 -is_a: has_participant +is_a: has_participant ! has participant created_by: pg creation_date: 2020-06-08T17:21:33Z @@ -132,8 +142,8 @@ name: allelopath of subset: ro-eco xref: RO:0002555 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Allelopathy xsd:string -property_value: seeAlso http://eol.org/schema/terms/allelopathyYes xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Allelopathy" xsd:string +property_value: seeAlso "http://eol.org/schema/terms/allelopathyYes" xsd:string property_value: seeAlso "x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -196,6 +206,26 @@ domain: CL:0000540 is_a: has_presynaptic_terminal_in ! has presynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: before +name: before +comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) +subset: ro-eco +xref: RO:0002083 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + +[Typedef] +id: before_or_simultaneous_with +name: before or simultaneous with +comment: Primitive instance level timing relation between events +subset: ro-eco +xref: RO:0002081 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "<=" xsd:string +is_a: temporally_related_to ! temporally related to + [Typedef] id: biomechanically_related_to name: biomechanically related to @@ -216,7 +246,7 @@ xref: RO:0002437 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string +property_value: seeAlso "http://eol.org/schema/terms/interactsWith" xsd:string domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -232,7 +262,7 @@ subset: ro-eco xref: RO:0002007 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: bounds_sequence_of @@ -254,10 +284,10 @@ subset: ro-eco xref: RO:0002380 property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso FMA:85994 xsd:string +property_value: seeAlso "FMA:85994" xsd:string property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of inverse_of: has_branching_part ! has branching part [Typedef] @@ -399,7 +429,7 @@ xref: RO:0002404 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within -is_a: preceded_by +is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of [Typedef] @@ -455,7 +485,7 @@ xref: RO:0002411 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: precedes +is_a: precedes ! precedes [Typedef] id: causally_upstream_of,_negative_effect @@ -530,6 +560,34 @@ property_value: IAO:0000112 "The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p property_value: IAO:0000116 "Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'." xsd:string is_a: causally_related_to ! causally related to +[Typedef] +id: characteristic_of +name: characteristic of +def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] +comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. +xref: RO:0000052 +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string +property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_functional: true +is_a: characteristic_of_part_of ! characteristic of part of +inverse_of: has_characteristic ! has characteristic + +[Typedef] +id: characteristic_of_part_of +name: characteristic of part of +def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] +xref: RO:0002314 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000118 "inheres in part of" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ +is_a: depends_on ! depends on + [Typedef] id: child_nucleus_of name: child nucleus of @@ -598,7 +656,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002441 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -613,7 +671,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part [Typedef] id: condition_ameliorated_by @@ -647,7 +705,7 @@ def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has p subset: ro-eco xref: RO:0002570 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 UBERON:cjm xsd:string +property_value: IAO:0000119 "UBERON:cjm" xsd:string property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string domain: BFO:0000040 range: BFO:0000040 @@ -679,8 +737,8 @@ def: "a is connected to b if and only if a and b are discrete structure, and the xref: RO:0002170 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -703,8 +761,8 @@ xref: RO:0002176 property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI domain: BFO:0000004 is_a: mereotopologically_related_to ! mereotopologically related to @@ -729,7 +787,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso FMA:85972 xsd:string +property_value: seeAlso "FMA:85972" xsd:string domain: BFO:0000004 range: BFO:0000004 is_symmetric: true @@ -813,6 +871,13 @@ domain: CL:0000540 is_a: has_postsynaptic_terminal_in ! has postsynaptic terminal in expand_expression_to: "BFO_0000051 some (\n GO_0030425 and BFO_0000051 some (\n http://purl.obolibrary.org/obo/GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: depends_on +name: depends on +xref: RO:0002502 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso BFO:0000169 + [Typedef] id: destabilizes_quantity_of name: destabilizes quantity of @@ -841,7 +906,7 @@ domain: RO:0002577 range: BFO:0000040 is_a: causally_influenced_by ! causally influenced by is_a: determined_by_part_of ! determined by part of -is_a: part_of +is_a: part_of ! part of inverse_of: determines ! determines [Typedef] @@ -889,7 +954,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "induced by" xsd:string property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 GO:0001759 xsd:string +property_value: IAO:0000119 "GO:0001759" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string domain: CARO:0000006 @@ -1295,6 +1360,15 @@ property_value: IAO:0000232 "Do not use this relation directly. It is intended a created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T00:00:32Z +[Typedef] +id: disposition_of +name: disposition of +def: "inverse of has disposition" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +subset: RO:0002259 +xref: RO:0000092 +is_a: characteristic_of ! characteristic of + [Typedef] id: distributary_of name: distributary of @@ -1307,7 +1381,7 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Distributary" xsd:string is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -1331,6 +1405,26 @@ property_value: IAO:0000116 "Individual ontologies should provide their own cons property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: connected_to ! connected to +[Typedef] +id: during_which_ends +name: during which ends +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002084 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: ends_during ! ends during + +[Typedef] +id: during_which_starts +name: during which starts +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +subset: ro-eco +xref: RO:0002088 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_a: temporally_related_to ! temporally related to +inverse_of: starts_during ! starts during + [Typedef] id: eats name: eats @@ -1365,7 +1459,7 @@ id: ectoparasite_of name: ectoparasite of def: "A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host" [] xref: RO:0002632 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_ectoparasite ! has ectoparasite @@ -1386,7 +1480,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002333 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: enables @@ -1414,36 +1508,81 @@ is_a: functionally_related_to ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z +[Typedef] +id: encompasses +name: encompasses +comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. +xref: RO:0002085 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "di" xsd:string +is_transitive: true +is_a: during_which_starts ! during which starts +inverse_of: happens_during ! happens during + [Typedef] id: endoparasite_of name: endoparasite of synonym: "lives inside of" RELATED [] xref: RO:0002634 property_value: IAO:0000119 "A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system" xsd:string -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: parasite_of ! parasite of inverse_of: has_endoparasite ! has endoparasite [Typedef] id: ends +name: ends +def: "inverse of ends with" [] subset: ro-eco xref: RO:0002229 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: ends_after +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +xref: RO:0002086 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: ends_during +name: ends during +comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). +subset: ro-eco +xref: RO:0002093 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "o" xsd:string +property_value: IAO:0000118 "overlaps" xsd:string +is_a: temporally_related_to ! temporally related to [Typedef] id: ends_with +name: ends with +def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "finished by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: epiphyte_of name: epiphyte of def: "An interaction relationship wherein a plant or algae is living on the outside surface of another plant." [] xref: RO:0008501 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Epiphyte xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Epiphyte" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with inverse_of: has_epiphyte ! has epiphyte @@ -1493,6 +1632,20 @@ xref: RO:0002354 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of +[Typedef] +id: function_of +name: function of +def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000079 +property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "function_of" xsd:string +property_value: IAO:0000118 "is function of" xsd:string +domain: BFO:0000034 +is_a: characteristic_of ! characteristic of +inverse_of: has_function ! has function + [Typedef] id: functionally_related_to name: functionally related to @@ -1505,17 +1658,43 @@ property_value: IAO:0000232 "This is a grouping relation that collects relations id: genetically_interacts_with name: genetically interacts with xref: RO:0002435 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0208 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0208" xsd:anyURI property_value: IAO:0000116 "An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso ECO:0000316 is_symmetric: true is_a: interacts_with ! interacts with +[Typedef] +id: happens_during +name: happens during +comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +xref: RO:0002092 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "d" xsd:string +property_value: IAO:0000118 "during" xsd:string +is_transitive: true +is_a: ends_during ! ends during +is_a: starts_during ! starts during + [Typedef] id: has_2D_boundary +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] xref: RO:0002002 +property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "has boundary" xsd:string +property_value: IAO:0000118 "has_2D_boundary" xsd:string +property_value: RO:0001900 RO:0001901 +domain: BFO:0000040 +range: BFO:0000141 is_a: mereotopologically_related_to ! mereotopologically related to [Typedef] @@ -1528,7 +1707,7 @@ xref: RO:0002248 property_value: IAO:0000112 "Any portion of roundup 'has active ingredient' some glyphosate" xsd:string domain: BFO:0000040 range: BFO:0000040 -is_a: has_part +is_a: has_part ! has part inverse_of: active_ingredient_in ! active ingredient in [Typedef] @@ -1540,6 +1719,13 @@ property_value: IAO:0000112 "penicillin allergy (DOID:0060520) has allergic trig range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_application_role +name: has application role +def: "c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)" [] +xref: RO:0002261 +is_a: has_role ! has role + [Typedef] id: has_autoimmune_trigger name: has autoimmune trigger @@ -1548,6 +1734,13 @@ xref: RO:0001023 range: BFO:0000040 is_a: causes_or_contributes_to_condition ! causes or contributes to condition +[Typedef] +id: has_biological_role +name: has biological role +def: "c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)" [] +xref: RO:0002260 +is_a: has_role ! has role + [Typedef] id: has_branching_part name: has branching part @@ -1557,12 +1750,30 @@ subset: RO:0002259 xref: RO:0002569 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true -is_a: has_part +is_a: has_part ! has part is_a: in_branching_relationship_with ! in branching relationship with [Typedef] id: has_characteristic +name: has characteristic +def: "Inverse of characteristic_of" [] xref: RO:0000053 +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 +is_inverse_functional: true + +[Typedef] +id: has_chemical_role +name: has chemical role +def: "c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)" [] +xref: RO:0002262 +is_a: has_role ! has role [Typedef] id: has_component @@ -1575,7 +1786,7 @@ property_value: IAO:0000116 "The definition of 'has component' is still under di property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part +is_a: has_part ! has part [Typedef] id: has_component_activity @@ -1593,7 +1804,7 @@ def: "X 'has component participant' Y means X 'has participant' Y and there is a xref: RO:0002238 property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 property_value: IAO:0000232 "This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part).\n\nIf you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'." xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_component_process @@ -1619,7 +1830,7 @@ is_a: in_branching_relationship_with ! in branching relationship with id: has_dendrite_location name: has dendrite location xref: RO:0002360 -property_value: http://purl.org/dc/terms/source http://neurolex.org/wiki/Property:DendriteLocation xsd:anyURI +property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps @@ -1665,10 +1876,20 @@ name: has disease def: "A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." [] xref: RO:0016002 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:44Z xsd:dateTime -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:44Z" xsd:dateTime +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string is_a: has_phenotype_or_disease ! has phenotype or disease +[Typedef] +id: has_disposition +name: has disposition +def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] +xref: RO:0000091 +domain: BFO:0000004 +range: BFO:0000016 +is_a: has_characteristic ! has characteristic +inverse_of: disposition_of ! disposition of + [Typedef] id: has_ectoparasite name: has ectoparasite @@ -1724,7 +1945,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included)" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ended by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_end_sequence_of ! is end sequence of @@ -1748,8 +1969,8 @@ id: has_exposure_medium name: has exposure medium def: "X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y." [] xref: RO:0016004 -property_value: http://purl.org/dc/elements/1.1/date 2021-12-14T20:41:45Z xsd:dateTime -property_value: IAO:0000119 ExO:0000083 xsd:string +property_value: http://purl.org/dc/elements/1.1/date "2021-12-14T20:41:45Z" xsd:dateTime +property_value: IAO:0000119 "ExO:0000083" xsd:string is_a: related_via_exposure_to ! related via exposure to created_by: https://orcid.org/0000-0002-7463-6306 @@ -1758,7 +1979,7 @@ id: has_exposure_receptor name: has exposure receptor def: "A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event." [] xref: RO:0002240 -property_value: IAO:0000119 ExO:0000001 xsd:string +property_value: IAO:0000119 "ExO:0000001" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1766,7 +1987,7 @@ id: has_exposure_route name: has exposure route def: "A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor" [] xref: RO:0002242 -property_value: IAO:0000119 ExO:0000055 xsd:string +property_value: IAO:0000119 "ExO:0000055" xsd:string is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1786,7 +2007,7 @@ id: has_exposure_stressor name: has exposure stressor def: "A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event." [] xref: RO:0002241 -property_value: IAO:0000119 ExO:0000000 xsd:string +property_value: IAO:0000119 "ExO:0000000" xsd:string is_a: has_exposure_stimulus ! has exposure stimulus [Typedef] @@ -1794,7 +2015,7 @@ id: has_exposure_transport_path name: has exposure transport path def: "A broad relationship between an exposure event or process and the course takes from the source to the target." [] xref: RO:0002243 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ExO_0000004 xsd:anyURI +property_value: IAO:0000119 "http://purl.obolibrary.org/obo/ExO_0000004" xsd:anyURI is_a: related_via_exposure_to ! related via exposure to [Typedef] @@ -1817,6 +2038,18 @@ name: has flowers visited by xref: RO:0002623 is_a: visited_by ! visited by +[Typedef] +id: has_function +name: has function +def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] +xref: RO:0000085 +property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string +property_value: IAO:0000118 "has_function" xsd:string +domain: BFO:0000004 +range: BFO:0000034 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_habitat name: has habitat @@ -1850,7 +2083,7 @@ def: "X 'has host' y if and only if: x is an organism, y is an organism, and x c subset: ro-eco xref: RO:0002454 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso http://eol.org/schema/terms/hasHost xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasHost" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -1866,7 +2099,7 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string domain: BFO:0000015 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: input_of ! input of [Typedef] @@ -1886,7 +2119,7 @@ xref: RO:0002505 property_value: IAO:0000112 "'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has intermediate product" xsd:string -is_a: has_participant +is_a: has_participant ! has participant [Typedef] id: has_intracellular_endoparasite @@ -1965,6 +2198,15 @@ inverse_of: is_causal_somatic_mutation_in ! is causal somatic mutation in created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-11-05T02:46:07Z +[Typedef] +id: has_member +name: has member +def: "has member is a mereological relation between a collection and an item." [] +xref: RO:0002351 +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: has_part ! has part + [Typedef] id: has_mesoparasite name: has mesoparasite @@ -1979,7 +2221,7 @@ name: has muscle antagonist def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] xref: RO:0002568 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Antagonist_(muscle) xsd:string +property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string is_a: biomechanically_related_to ! biomechanically related to [Typedef] @@ -1988,7 +2230,7 @@ name: has muscle insertion def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] xref: RO:0002373 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/insertion domain: CARO:0000003 {http://purl.obolibrary.org/obo/IAO_0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} is_a: attached_to ! attached to @@ -2000,7 +2242,7 @@ name: has muscle origin def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] xref: RO:0002372 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 Wikipedia:Insertion_(anatomy) xsd:string +property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string property_value: seeAlso http://dbpedia.org/property/origin domain: CARO:0000003 {comment="We need to import uberon muscle to create a stricter domain constraint"} is_a: attached_to ! attached to @@ -2039,7 +2281,7 @@ xref: RO:0002234 property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string -is_a: has_participant +is_a: has_participant ! has participant inverse_of: output_of ! output of [Typedef] @@ -2052,10 +2294,22 @@ is_a: parasitized_by ! parasitized by [Typedef] id: has_part +name: has part +def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true is_a: overlaps ! overlaps [Typedef] @@ -2089,7 +2343,18 @@ creation_date: 2017-11-05T02:46:57Z [Typedef] id: has_participant +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 +range: BFO:0000002 [Typedef] id: has_pathogen @@ -2116,9 +2381,9 @@ id: has_phenotype_or_disease name: has phenotype or disease xref: RO:0016001 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-7463-6306 -property_value: http://purl.org/dc/elements/1.1/date 2021-11-05T17:30:14Z xsd:dateTime +property_value: http://purl.org/dc/elements/1.1/date "2021-11-05T17:30:14Z" xsd:dateTime property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease." xsd:string -property_value: seeAlso https://github.com/oborel/obo-relations/issues/478 xsd:string +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/478" xsd:string [Typedef] id: has_plasma_membrane_part @@ -2134,7 +2399,7 @@ property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 property_value: RO:0001900 RO:0001901 domain: CARO:0000006 range: CARO:0000006 -is_a: has_part +is_a: has_part ! has part expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] [Typedef] @@ -2230,7 +2495,7 @@ name: has primary input or output def: "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0004007 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:17Z @@ -2245,6 +2510,17 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z +[Typedef] +id: has_quality +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +xref: RO:0000086 +property_value: IAO:0000112 "this apple has quality this red color" xsd:string +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "has_quality" xsd:string +range: BFO:0000019 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -2255,6 +2531,18 @@ is_a: regulated_by ! regulated by created_by: dos creation_date: 2017-05-24T09:30:46Z +[Typedef] +id: has_role +name: has role +def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] +xref: RO:0000087 +property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "has_role" xsd:string +domain: BFO:0000004 +range: BFO:0000023 +is_a: has_characteristic ! has characteristic + [Typedef] id: has_sensory_dendrite_in name: has sensory dendrite in @@ -2279,7 +2567,7 @@ property_value: IAO:0000118 "has supporting framework" xsd:string property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string domain: CARO:0000003 range: CARO:0000006 {http://purl.obolibrary.org/obo/IAO_0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} -is_a: has_part +is_a: has_part ! has part inverse_of: skeleton_of ! skeleton of is_asymmetric: true @@ -2308,7 +2596,7 @@ id: has_small_molecule_regulator name: has small molecule regulator def: "a relation between a process and a continuant, in which the process is regulated by the small molecule continuant" [] xref: RO:0012000 -is_a: has_participant +is_a: has_participant ! has participant inverse_of: is_small_molecule_regulator_of ! is small molecule regulator of created_by: pg creation_date: 2020-04-22T20:27:26Z @@ -2348,7 +2636,7 @@ property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/co property_value: IAO:0000112 "Every CDS has as a start sequence the start codon for that transcript" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: has_subsequence ! has subsequence inverse_of: is_start_sequence_of ! is start sequence of @@ -2361,10 +2649,10 @@ xref: RO:0002524 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "contains" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: bounds_sequence_of ! bounds sequence of -is_a: has_part +is_a: has_part ! has part is_a: overlaps_sequence_of ! overlaps sequence of inverse_of: is_subsequence_of ! is subsequence of @@ -2475,8 +2763,8 @@ synonym: "hyperparasitoid of" NARROW [] xref: RO:0002553 property_value: IAO:0000116 "Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://eol.org/schema/terms/hyperparasitoidOf xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Hyperparasite xsd:string +property_value: IAO:0000119 "http://eol.org/schema/terms/hyperparasitoidOf" xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Hyperparasite" xsd:string is_a: has_host ! has host inverse_of: hyperparasitized_by ! hyperparasitized by @@ -2510,7 +2798,7 @@ xref: RO:0002405 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of -is_a: immediately_preceded_by +is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of [Typedef] @@ -2521,18 +2809,30 @@ xref: RO:0002412 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of -is_a: immediately_precedes +is_a: immediately_precedes ! immediately precedes [Typedef] id: immediately_preceded_by +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: preceded_by ! preceded by +inverse_of: immediately_precedes ! immediately precedes [Typedef] id: immediately_precedes +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 +is_a: precedes ! precedes [Typedef] id: imports @@ -2554,7 +2854,7 @@ property_value: IAO:0000232 "Do not use this relation directly. It is ended as a property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_a: mereotopologically_related_to ! mereotopologically related to @@ -2696,7 +2996,7 @@ subset: RO:0002259 xref: RO:0002352 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: interacts_with @@ -2705,12 +3005,12 @@ def: "A relationship that holds between two entities in which the processes exec subset: ro-eco synonym: "in pairwise interaction with" EXACT [] xref: RO:0002434 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI +property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 range: BFO:0000040 is_symmetric: true @@ -2722,7 +3022,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002443 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "This relation groups a pair of inverse relations, parasite of and parasitized by" xsd:string is_a: symbiotically_interacts_with ! symbiotically interacts with @@ -2731,7 +3031,7 @@ id: intercellular_endoparasite_of name: intercellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells." [] xref: RO:0002638 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intercellular_endoparasite ! has intercellular endoparasite @@ -2740,7 +3040,7 @@ id: intracellular_endoparasite_of name: intracellular endoparasite of def: "A sub-relation of endoparasite-of in which the parasite inhabits host cells." [] xref: RO:0002640 -property_value: IAO:0000119 "Types" +property_value: IAO:0000119 Types is_a: endoparasite_of ! endoparasite of inverse_of: has_intracellular_endoparasite ! has intracellular endoparasite @@ -2754,7 +3054,7 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso Involved:in is_a: involved_in_or_involved_in_regulation_of ! involved in or involved in regulation of -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: involved_in_negative_regulation_of @@ -2936,7 +3236,7 @@ xref: RO:0002520 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000116 "In the SO paper, this was defined as an instance-type relation" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: has_subsequence ! has subsequence [Typedef] @@ -2969,7 +3269,7 @@ xref: RO:0002519 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3071,7 +3371,7 @@ xref: RO:0002517 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_transitive: true is_a: is_subsequence_of ! is subsequence of @@ -3087,7 +3387,7 @@ property_value: IAO:0000118 "contained by" xsd:string is_transitive: true is_a: is_bound_by_sequence_of ! is bound by sequence of is_a: overlaps_sequence_of ! overlaps sequence of -is_a: part_of +is_a: part_of ! part of [Typedef] id: is_substance_that_treats @@ -3134,7 +3434,7 @@ inverse_of: has_vector ! has vector id: kills name: kills xref: RO:0002626 -property_value: IAO:0000119 https://github.com/jhpoelen/eol-globi-data/issues/143 xsd:string +property_value: IAO:0000119 "https://github.com/jhpoelen/eol-globi-data/issues/143" xsd:string is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: is_killed_by ! is killed by @@ -3143,7 +3443,7 @@ id: kleptoparasite_of name: kleptoparasite of def: "A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material" [] xref: RO:0008503 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Kleptoparasitism xsd:string +property_value: IAO:0000119 "https://en.wikipedia.org/wiki/Kleptoparasitism" xsd:string is_a: parasite_of ! parasite of inverse_of: kleptoparasitized_by ! kleptoparasitized by @@ -3178,9 +3478,9 @@ def: "x lumen_of y iff x is the space or substance that is part of y and does no subset: ro-eco xref: RO:0002571 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:cjm xsd:string +property_value: IAO:0000119 "GOC:cjm" xsd:string range: BFO:0000040 -is_a: part_of +is_a: part_of ! part of [Typedef] id: luminal_space_of @@ -3203,7 +3503,20 @@ property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 is_a: in_branching_relationship_with ! in branching relationship with -is_a: part_of +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +def: "is member of is a mereological relation between a item and a collection." [] +xref: RO:0002350 +property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string +property_value: IAO:0000118 "is member of" xsd:string +property_value: IAO:0000118 "member part of" xsd:string +property_value: IAO:0000119 "SIO" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: part_of ! part of +inverse_of: has_member ! has member [Typedef] id: mereotopologically_related_to @@ -3227,7 +3540,7 @@ id: molecularly_interacts_with name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] xref: RO:0002436 -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "binds" xsd:string property_value: IAO:0000118 "molecularly binds with" xsd:string @@ -3242,7 +3555,7 @@ def: "An interaction relationship between two organisms living together in more subset: ro-eco xref: RO:0002442 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI is_a: symbiotically_interacts_with ! symbiotically interacts with [Typedef] @@ -3310,7 +3623,7 @@ xref: RO:0002012 domain: BFO:0000003 range: BFO:0000003 is_a: causally_upstream_of_or_within ! causally upstream of or within -is_a: part_of +is_a: part_of ! part of [Typedef] id: occurs_across @@ -3330,7 +3643,7 @@ subset: RO:0002259 xref: RO:0002353 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: functionally_related_to ! functionally related to -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: overlaps @@ -3366,7 +3679,7 @@ xref: RO:0002444 property_value: IAO:0000112 "Pediculus humanus capitis parasite of human" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "parasitizes" xsd:string -property_value: seeAlso http://eol.org/schema/terms/parasitizes xsd:string +property_value: seeAlso "http://eol.org/schema/terms/parasitizes" xsd:string is_a: has_host ! has host is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction inverse_of: parasitized_by ! parasitized by @@ -3380,7 +3693,7 @@ xref: RO:0002445 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has parasite" xsd:string property_value: IAO:0000118 "parasitised by" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasParasite xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasParasite" xsd:string is_a: host_of ! host of is_a: interacts_with_via_parasite-host_interaction ! interacts with via parasite-host interaction @@ -3394,11 +3707,22 @@ inverse_of: has_parasitoid ! has parasitoid [Typedef] id: part_of +name: part of +def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 property_value: RO:0040042 BFO:0000002 property_value: RO:0040042 BFO:0000003 property_value: RO:0040042 BFO:0000004 @@ -3408,7 +3732,10 @@ property_value: RO:0040042 BFO:0000020 property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +is_transitive: true is_a: overlaps ! overlaps +inverse_of: has_part ! has part [Typedef] id: part_of_developmental_precursor_of @@ -3443,7 +3770,17 @@ is_a: overlaps ! overlaps [Typedef] id: participates_in +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 +range: BFO:0000003 +inverse_of: has_participant ! has participant [Typedef] id: participates_in_a_abiotic-biotic_interaction_with @@ -3474,7 +3811,7 @@ name: partner in xref: RO:0002461 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target" xsd:string -is_a: participates_in +is_a: participates_in ! participates in [Typedef] id: pathogen_of @@ -3513,7 +3850,7 @@ xref: RO:0002456 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has polinator" xsd:string property_value: IAO:0000118 "is target of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/hasPollinator xsd:string +property_value: seeAlso "http://eol.org/schema/terms/hasPollinator" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with [Typedef] @@ -3525,7 +3862,7 @@ property_value: IAO:0000112 "Bees pollinate Flowers" xsd:string property_value: IAO:0000116 "This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "is subject of pollination interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/pollinates xsd:string +property_value: seeAlso "http://eol.org/schema/terms/pollinates" xsd:string is_a: mutualistically_interacts_with ! mutualistically interacts with inverse_of: pollinated_by ! pollinated by @@ -3565,14 +3902,32 @@ is_a: regulates_characteristic ! regulates characteristic [Typedef] id: preceded_by +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 +property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: ends_after ! ends after +inverse_of: precedes ! precedes [Typedef] id: precedes +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -is_a: temporally_related_to +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_transitive: true +is_a: temporally_related_to ! temporally related to [Typedef] id: preyed_upon_by @@ -3584,8 +3939,8 @@ xref: RO:0002458 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has predator" xsd:string property_value: IAO:0000118 "is target of predation interaction with" xsd:string -property_value: seeAlso http://eol.org/schema/terms/HasPredator xsd:string -property_value: seeAlso http://polytraits.lifewatchgreece.eu/terms/PRED xsd:string +property_value: seeAlso "http://eol.org/schema/terms/HasPredator" xsd:string +property_value: seeAlso "http://polytraits.lifewatchgreece.eu/terms/PRED" xsd:string is_a: trophically_interacts_with ! trophically interacts with [Typedef] @@ -3601,8 +3956,8 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000117 https://orcid.org/0000-0003-3138-4118 property_value: IAO:0000118 "is subject of predation interaction with" xsd:string property_value: IAO:0000118 "preys upon" xsd:string -property_value: seeAlso http://eol.org/schema/terms/preysUpon xsd:string -property_value: seeAlso http://www.inaturalist.org/observations/2942824 xsd:string +property_value: seeAlso "http://eol.org/schema/terms/preysUpon" xsd:string +property_value: seeAlso "http://www.inaturalist.org/observations/2942824" xsd:string is_a: trophically_interacts_with ! trophically interacts with inverse_of: preyed_upon_by ! preyed upon by @@ -3655,6 +4010,19 @@ xref: RO:0002469 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: trophically_interacts_with ! trophically interacts with +[Typedef] +id: quality_of +name: quality of +def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000080 +property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string +property_value: IAO:0000118 "is quality of" xsd:string +property_value: IAO:0000118 "quality_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_quality ! has quality + [Typedef] id: realizable_has_basis_in name: realizable has basis in @@ -3677,7 +4045,7 @@ property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string -property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI +property_value: seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" xsd:anyURI domain: BFO:0000017 range: BFO:0000015 is_a: causally_related_to ! causally related to @@ -3870,7 +4238,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: CARO:0000003 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -3913,7 +4281,7 @@ id: results_in_changes_to_anatomical_or_cellular_structure name: results in changes to anatomical or cellular structure def: "p has anatomical participant c iff p has participant c, and c is an anatomical entity" [] xref: RO:0040036 -is_a: has_participant +is_a: has_participant ! has participant created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-09-26T01:08:58Z @@ -3961,7 +4329,7 @@ xref: RO:0002296 property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.geneontology.org/GO.doc.development.shtml xsd:anyURI +property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4033,7 +4401,7 @@ property_value: IAO:0000112 "an annotation of gene X to anatomical structure for property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: formed_as_result_of ! formed as result of @@ -4070,7 +4438,7 @@ property_value: IAO:0000112 " an annotation of gene X to cell maturation with re property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4086,7 +4454,7 @@ property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string +property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -4169,6 +4537,19 @@ property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_f property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: related_via_localization_to ! related via localization to +[Typedef] +id: role_of +name: role of +def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] +comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. +xref: RO:0000081 +property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string +property_value: IAO:0000118 "is role of" xsd:string +property_value: IAO:0000118 "role_of" xsd:string +is_a: characteristic_of ! characteristic of +inverse_of: has_role ! has role + [Typedef] id: root_parasite_of name: root parasite of @@ -4224,7 +4605,7 @@ property_value: IAO:0000112 "Every UTR is adjacent to a CDS of the same transcri property_value: IAO:0000112 "Two consecutive DNA residues are sequentially adjacent" xsd:string property_value: IAO:0000112 "Two exons on a processed transcript that were previously connected by an intron are adjacent" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI is_a: does_not_overlap_sequence_of ! does not overlap sequence of [Typedef] @@ -4234,12 +4615,23 @@ def: "A relation that holds between two entities that have the property of being xref: RO:0002514 property_value: http://purl.org/spar/cito/citesAsAuthority http://biorxiv.org/content/early/2014/06/27/006650.abstract property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20226267 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267" xsd:anyURI property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string property_value: IAO:0000232 "The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene." xsd:string domain: RO:0002532 range: RO:0002532 +[Typedef] +id: simultaneous_with +name: simultaneous with +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +xref: RO:0002082 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +is_transitive: true +is_a: before_or_simultaneous_with ! before or simultaneous with + [Typedef] id: skeleton_of name: skeleton of @@ -4249,7 +4641,7 @@ xref: RO:0002576 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: CARO:0000003 range: CARO:0000003 -is_a: part_of +is_a: part_of ! part of [Typedef] id: spatially_coextensive_with @@ -4273,7 +4665,7 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: mereotopologically_related_to ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] @@ -4290,17 +4682,53 @@ is_a: directly_positively_regulates_quantity_of ! directly positively regulates [Typedef] id: starts +name: starts +def: "inverse of starts with" [] subset: ro-eco xref: RO:0002223 +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of +property_value: IAO:0000119 "Allen" xsd:string +is_a: part_of ! part of +is_a: temporally_related_to ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_before +name: starts before +subset: ro-eco +xref: RO:0002089 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: temporally_related_to ! temporally related to + +[Typedef] +id: starts_during +name: starts during +comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) +subset: ro-eco +xref: RO:0002091 +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "io" xsd:string +domain: BFO:0000003 +range: BFO:0000003 +is_a: temporally_related_to ! temporally related to [Typedef] id: starts_with +name: starts with +def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 +property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_part +property_value: IAO:0000118 "started by" xsd:string +is_transitive: true +is_a: has_part ! has part +is_a: temporally_related_to ! temporally related to [Typedef] id: stem_parasite_of @@ -4318,7 +4746,7 @@ property_value: IAO:0000116 "X subcluster_of Y iff: X and Y are clusters/groups; property_value: IAO:0000117 https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000232 "This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics." xsd:string is_transitive: true -is_a: part_of +is_a: part_of ! part of [Typedef] id: subject_participant_in @@ -4366,7 +4794,7 @@ def: "A biotic interaction in which the two organisms live together in more or l subset: ro-eco xref: RO:0002440 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19278549 xsd:anyURI +property_value: IAO:0000119 "http://www.ncbi.nlm.nih.gov/pubmed/19278549" xsd:anyURI property_value: IAO:0000232 "We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism" xsd:string is_symmetric: true is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with @@ -4518,11 +4946,27 @@ is_a: partner_in ! partner in [Typedef] id: temporally_related_to +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco xref: RO:0002222 -property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI +property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 +range: BFO:0000003 + +[Typedef] +id: towards +name: towards +def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] +xref: RO:0002503 +property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +is_a: depends_on ! depends on [Typedef] id: transformation_of @@ -4592,11 +5036,11 @@ property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tributary xsd:string -property_value: IAO:0000119 http://www.medindia.net/glossary/venous_tributary.htm xsd:string +property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string +property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso http://en.wikipedia.org/wiki/Tributary xsd:anyURI +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI is_a: connected_to ! connected to is_a: in_branching_relationship_with ! in branching relationship with @@ -4629,7 +5073,7 @@ is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a bioti id: visits name: visits xref: RO:0002618 -property_value: seeAlso https://github.com/oborel/obo-relations/issues/74 xsd:anyURI +property_value: seeAlso "https://github.com/oborel/obo-relations/issues/74" xsd:anyURI is_a: participates_in_a_biotic-biotic_interaction_with ! participates in a biotic-biotic interaction with inverse_of: visited_by ! visited by diff --git a/subsets/ro-time-interval.owl b/subsets/ro-time-interval.owl index 85959a1e..286fb05e 100644 --- a/subsets/ro-time-interval.owl +++ b/subsets/ro-time-interval.owl @@ -27,6 +27,12 @@ + + + + + + @@ -159,6 +165,12 @@ + + + + + + @@ -258,6 +270,20 @@ + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + @@ -271,8 +297,10 @@ part_of + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -281,11 +309,25 @@ + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + BFO:0000051 has_part + has part @@ -293,9 +335,21 @@ + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 preceded_by + preceded by @@ -304,9 +358,35 @@ + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 precedes + precedes + + + + + + + + + + + inheres in + this fragility is a characteristic of this vase + this red color is a characteristic of this apple + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + inheres_in + + RO:0000052 + characteristic_of + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. + characteristic of @@ -314,8 +394,19 @@ + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + Inverse of characteristic_of + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + RO:0000053 has_characteristic + has characteristic @@ -323,8 +414,18 @@ + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in RO:0000056 participates_in + participates in @@ -332,8 +433,153 @@ + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 has_participant + has participant + + + + + + + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + RO:0000079 + function_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + RO:0000080 + quality_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of + + + + + + + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + RO:0000081 + role_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of + + + + + + + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + RO:0000085 + has_function + has function + + + + + + + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + RO:0000086 + has_quality + has quality + + + + + + + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + RO:0000087 + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + RO:0000091 + has_disposition + has disposition + + + + + + + + + inverse of has disposition + RO:0000092 + + disposition_of + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of @@ -398,9 +644,20 @@ + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of surface of + RO:0002000 2D_boundary_of + 2D boundary of @@ -409,9 +666,19 @@ + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + RO:0002002 has_2D_boundary + has 2D boundary @@ -802,11 +1069,138 @@ Examples include: the relationship between two channels collected simultaneously + + + + + David Osumi-Sutherland + <= + RO:0002081 + + before_or_simultaneous_with + Primitive instance level timing relation between events + before or simultaneous with + + + + + + + + + + + David Osumi-Sutherland + RO:0002082 + + simultaneous_with + t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) + simultaneous with + + + + + + + + + + David Osumi-Sutherland + RO:0002083 + + before + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) + before + + + + + + + + + + David Osumi-Sutherland + RO:0002084 + + during_which_ends + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which ends + + + + + + + + + + + + di + RO:0002085 + encompasses + Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + encompasses + + + + + + + + + + David Osumi-Sutherland + RO:0002086 + + ends_after + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + David Osumi-Sutherland + starts_at_end_of RO:0002087 immediately_preceded_by + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + + David Osumi-Sutherland + RO:0002088 + + during_which_starts + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. + during which starts + + + + + + + + + + David Osumi-Sutherland + RO:0002089 + + starts_before + starts before @@ -814,11 +1208,71 @@ Examples include: the relationship between two channels collected simultaneously + + David Osumi-Sutherland + ends_at_start_of + meets RO:0002090 immediately_precedes + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + David Osumi-Sutherland + io + RO:0002091 + + starts_during + X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) + starts during + + + + + + + + + + + David Osumi-Sutherland + d + during + RO:0002092 + + + + + happens_during + X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) + happens during + + + + + + + + + David Osumi-Sutherland + o + overlaps + RO:0002093 + + ends_during + X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). + ends during @@ -1815,12 +2269,18 @@ N1 SubclassOf ( + + + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to @@ -1829,10 +2289,17 @@ N1 SubclassOf ( + + + + inverse of starts with + Chris Mungall + Allen RO:0002223 starts + starts @@ -1841,10 +2308,18 @@ N1 SubclassOf ( + + + Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor + + x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + started by RO:0002224 starts_with + starts with @@ -1908,10 +2383,16 @@ N1 SubclassOf ( + + + + inverse of ends with + Chris Mungall RO:0002229 ends + ends @@ -1920,10 +2401,17 @@ N1 SubclassOf ( + + + + x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall + finished by RO:0002230 ends_with + ends with @@ -2278,6 +2766,42 @@ If you need an axiom that says 'has_participant min 2 object', you sho + + + + + c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) + RO:0002260 + has_biological_role + has biological role + + + + + + + + + c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) + RO:0002261 + has_application_role + has application role + + + + + + + + + c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) + RO:0002262 + has_chemical_role + has chemical role + + + + @@ -2591,6 +3115,24 @@ where + + + + + q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of characteristic of part of + + inheres in part of + + + RO:0002314 + characteristic_of_part_of + characteristic of part of + + + + + @@ -3026,6 +3568,39 @@ However, this is not possible in OWL. We instead make this relation a sub-relati + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + RO:0002350 + member_of + member of + + + + + + + + + + has member is a mereological relation between a collection and an item. + SIO + + RO:0002351 + has_member + has member + + + + @@ -4475,6 +5050,33 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + RO:0002502 + depends_on + depends on + + + + + + + + + + q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 + This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. + + + RO:0002503 + towards + towards + + + + @@ -7513,6 +8115,12 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + @@ -7525,12 +8133,30 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + + + + + + + + + + + + + + diff --git a/subsets/ro-time-interval.tsv b/subsets/ro-time-interval.tsv new file mode 100644 index 00000000..a57fc830 --- /dev/null +++ b/subsets/ro-time-interval.tsv @@ -0,0 +1,51 @@ +?x ?label +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid1 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid18 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid22 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid26 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid33 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid37 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid40 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid5 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid52 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid58 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid61 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid64 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid67 +_:Bee8e8d16X2D3c90X2D4f5eX2D8087X2Dc4dd64610129genid9 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/temporal-intervals.owl b/temporal-intervals.owl deleted file mode 100644 index bb7ee22f..00000000 --- a/temporal-intervals.owl +++ /dev/null @@ -1,326 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accidentally included in BFO 1.2 proposal - - should have been BFO_0000062 - obsolete preceded by - - - - - - - - - - - - - - - - - - - - - preceded by - x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - preceded by - - - - - - - - - - - precedes - x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - precedes - - - - - - - - - David Osumi-Sutherland - <= - Primitive instance level timing relation between events - before or simultaneous with - - - - - - - - - - David Osumi-Sutherland - t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with - - - - - - - - - - David Osumi-Sutherland - t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) - before - - - - - - - - - - David Osumi-Sutherland - Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which ends - - - - - - - - - - - - - - David Osumi-Sutherland - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - ends after - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - immediately preceded by - - - - - - - - - - David Osumi-Sutherland - Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which starts - - - - - - - - - - - - - - David Osumi-Sutherland - starts before - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - immediately precedes - - - - - - - - - - - David Osumi-Sutherland - io - X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) - starts during - - - - - - - - - - David Osumi-Sutherland - d - during - X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) - happens during - - - - - - - - - David Osumi-Sutherland - o - overlaps - X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). - ends during - - - - - - - - - - - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporally related to - - - - - - - - - - - inverse of starts with - Chris Mungall - Allen - starts - - - - - - - - - - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall - started by - starts with - - - - - - - - - - - inverse of ends with - Chris Mungall - ends - - - - - - - - - - - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall - finished by - ends with - - - - - - -